Re: [ccp4bb] Atom clashes in active site?

[Scott Horowitz]

Hi Andrew,

Here are those references:

for CH...O hydrogen bonds I'd recommend our review: "Carbon-Oxygen Hydrogen
Bonding in Biological Structure and Function" (2012)
http://www.jbc.org/content/287/50/41576.full

for chalcogen bonds, I don't know of a great recent review, but this recent
article (2016) has a whole bunch of references (listed under 19 and 20) on
it: https://www.ncbi.nlm.nih.gov/pubmed/27992115

Scott

On Tue, Dec 20, 2016 at 8:45 PM, Andrew Marshall <
andrew.c.marsh...@adelaide.edu.au> wrote:

> Hi Scott,
>
> That would be great if you have some references handy?
> Thanks very much,
>
> Andrew Marshall
> PhD Candidate
> Laboratory of Protein Crystallography
> Dept. of Molecular and Cellular Biology
> School of Biological Sciences
> The University of Adelaide
>
> On Wed, Dec 21, 2016 at 1:48 AM, Scott Horowitz 
> wrote:
>
>> Hi Andrew,
>>
>> Based on the atoms and distances you are mentioning, these don't sound
>> like steric clashes, but like a chalcogen bond between the S and O atoms,
>> and CH...O hydrogen bonds between the O and CH3. These are common and
>> well-accepted interactions, but unfortunately aren't usually treated as
>> such by refinement programs. Let me know if you want references for these
>> interaction types.
>>
>> Scott
>>
>> On Mon, Dec 19, 2016 at 8:48 PM, Andrew Marshall <
>> andrew.c.marsh...@adelaide.edu.au> wrote:
>>
>>> Hi all,
>>>
>>> Thank you for your suggestions. I tried the pdb file edit (making the
>>> offending atoms of both the ligand and the protein 'B' altconf), but it
>>> didn't seem to make any difference to their positions after a single round
>>> of refinement..?
>>> The atoms in the active site concern two acetyl groups - one from the
>>> substrate, acetyl-CoA, and the other from an acetylated cysteine in the
>>> protein - that I believe are poised ready for a condensation reaction. The
>>> closest contacts are between S and O(carbonyl) atoms (2.9A) and O and CH3
>>> (3.1A), but going off the density, I think these should be closer (more
>>> like 2.8 or 2.7A). It may be that I've trapped another reaction
>>> intermediate (which would be cool), but I don't think that fits the density
>>> quite as well. Any thoughts/ideas?
>>>
>>> Thanks,
>>>
>>> Andrew Marshall
>>> PhD Candidate
>>> Laboratory of Protein Crystallography
>>> Dept. of Molecular and Cellular Biology
>>> School of Biological Sciences
>>> The University of Adelaide
>>>
>>> On Tue, Dec 20, 2016 at 12:09 AM, Scott Horowitz 
>>> wrote:
>>>
 Hi Andrew,

 I'm curious- what are the atoms that are clashing? I worked on this
 sort of thing back in my Ph.D., and so I might have some useful tidbits if,
 for example, the S is clashing with a carbon of some sort.

 Thanks,
 Scott

 On Mon, Dec 19, 2016 at 12:39 AM, Andrew Marshall <
 andrew.c.marsh...@adelaide.edu.au> wrote:

> Hi all,
>
> I have a structure of a condensing enzyme with substrate bound. The
> active site is very tight, requiring some of the substrate atoms to clash
> with a catalytic cysteine. This means that although the substrate fits the
> density nicely upon manual real-space refinement, phenix recognises the
> clash, resulting in the displacement of substrate atoms so that they are
> outside the density. I can mostly fix this by using distance restraints,
> but I'd rather allow it to refine in a less biased manner, but ignore the
> clash. Is this a acceptable way forward? If so, is there a parameter I can
> edit to tell phenix to ignore clashes between these specific atoms?
>
> Thanks,
>
> Andrew Marshall
> PhD Candidate
> Laboratory of Protein Crystallography
> Dept. of Molecular and Cellular Biology
> School of Biological Sciences
> The University of Adelaide
>
>


 --
 Scott Horowitz, Ph.D.
 Postdoctoral Fellow

 University of Michigan
 Department of Molecular, Cellular, and Developmental Biology
 Bardwell lab
 830 N. University Ave, Room 4007
 Ann Arbor, MI 48109
 phone: 734-647-6683
 fax: 734-615-4226

>>>
>>>
>>
>>
>> --
>> Scott Horowitz, Ph.D.
>> Postdoctoral Fellow
>>
>> University of Michigan
>> Department of Molecular, Cellular, and Developmental Biology
>> Bardwell lab
>> 830 N. University Ave, Room 4007
>> Ann Arbor, MI 48109
>> phone: 734-647-6683
>> fax: 734-615-4226
>>
>
>


-- 
Scott Horowitz, Ph.D.
Postdoctoral Fellow

University of Michigan
Department of Molecular, Cellular, and Developmental Biology
Bardwell lab
830 N. University Ave, Room 4007
Ann Arbor, MI 48109
phone: 734-647-6683
fax: 734-615-4226

Re: [ccp4bb] Atom clashes in active site?

[Andrew Marshall]

Hi Scott,

That would be great if you have some references handy?
Thanks very much,

Andrew Marshall
PhD Candidate
Laboratory of Protein Crystallography
Dept. of Molecular and Cellular Biology
School of Biological Sciences
The University of Adelaide

On Wed, Dec 21, 2016 at 1:48 AM, Scott Horowitz  wrote:

> Hi Andrew,
>
> Based on the atoms and distances you are mentioning, these don't sound
> like steric clashes, but like a chalcogen bond between the S and O atoms,
> and CH...O hydrogen bonds between the O and CH3. These are common and
> well-accepted interactions, but unfortunately aren't usually treated as
> such by refinement programs. Let me know if you want references for these
> interaction types.
>
> Scott
>
> On Mon, Dec 19, 2016 at 8:48 PM, Andrew Marshall <
> andrew.c.marsh...@adelaide.edu.au> wrote:
>
>> Hi all,
>>
>> Thank you for your suggestions. I tried the pdb file edit (making the
>> offending atoms of both the ligand and the protein 'B' altconf), but it
>> didn't seem to make any difference to their positions after a single round
>> of refinement..?
>> The atoms in the active site concern two acetyl groups - one from the
>> substrate, acetyl-CoA, and the other from an acetylated cysteine in the
>> protein - that I believe are poised ready for a condensation reaction. The
>> closest contacts are between S and O(carbonyl) atoms (2.9A) and O and CH3
>> (3.1A), but going off the density, I think these should be closer (more
>> like 2.8 or 2.7A). It may be that I've trapped another reaction
>> intermediate (which would be cool), but I don't think that fits the density
>> quite as well. Any thoughts/ideas?
>>
>> Thanks,
>>
>> Andrew Marshall
>> PhD Candidate
>> Laboratory of Protein Crystallography
>> Dept. of Molecular and Cellular Biology
>> School of Biological Sciences
>> The University of Adelaide
>>
>> On Tue, Dec 20, 2016 at 12:09 AM, Scott Horowitz 
>> wrote:
>>
>>> Hi Andrew,
>>>
>>> I'm curious- what are the atoms that are clashing? I worked on this sort
>>> of thing back in my Ph.D., and so I might have some useful tidbits if, for
>>> example, the S is clashing with a carbon of some sort.
>>>
>>> Thanks,
>>> Scott
>>>
>>> On Mon, Dec 19, 2016 at 12:39 AM, Andrew Marshall <
>>> andrew.c.marsh...@adelaide.edu.au> wrote:
>>>
 Hi all,

 I have a structure of a condensing enzyme with substrate bound. The
 active site is very tight, requiring some of the substrate atoms to clash
 with a catalytic cysteine. This means that although the substrate fits the
 density nicely upon manual real-space refinement, phenix recognises the
 clash, resulting in the displacement of substrate atoms so that they are
 outside the density. I can mostly fix this by using distance restraints,
 but I'd rather allow it to refine in a less biased manner, but ignore the
 clash. Is this a acceptable way forward? If so, is there a parameter I can
 edit to tell phenix to ignore clashes between these specific atoms?

 Thanks,

 Andrew Marshall
 PhD Candidate
 Laboratory of Protein Crystallography
 Dept. of Molecular and Cellular Biology
 School of Biological Sciences
 The University of Adelaide


>>>
>>>
>>> --
>>> Scott Horowitz, Ph.D.
>>> Postdoctoral Fellow
>>>
>>> University of Michigan
>>> Department of Molecular, Cellular, and Developmental Biology
>>> Bardwell lab
>>> 830 N. University Ave, Room 4007
>>> Ann Arbor, MI 48109
>>> phone: 734-647-6683
>>> fax: 734-615-4226
>>>
>>
>>
>
>
> --
> Scott Horowitz, Ph.D.
> Postdoctoral Fellow
>
> University of Michigan
> Department of Molecular, Cellular, and Developmental Biology
> Bardwell lab
> 830 N. University Ave, Room 4007
> Ann Arbor, MI 48109
> phone: 734-647-6683
> fax: 734-615-4226
>

Re: [ccp4bb] Atom clashes in active site?

[Andrew Marshall]

Hi Pavel,

That worked a treat! Thanks again for your help,

Andrew Marshall
PhD Candidate
Laboratory of Protein Crystallography
Dept. of Molecular and Cellular Biology
School of Biological Sciences
The University of Adelaide

On Tue, Dec 20, 2016 at 3:18 PM, Pavel Afonine  wrote:

> Hi Andrew,
>
> yes, exactly as you describe: set distance_ideal to a meaningful value
> (approx. distance between density peaks, doesn't have to be very accurate),
> and set sigma to some large number, say 1 or so.
>
> Pavel
>
>
> On Mon, Dec 19, 2016 at 7:40 PM, Andrew Marshall <
> andrew.c.marsh...@adelaide.edu.au> wrote:
>
>> Hi Pavel,
>>
>> To define a weak bond, would you use "geometry_restraints.edits { ...
>> bond {... " , and just set a rough distance_ideal and a very high sigma
>> (like say 5A)?
>> Or are you referring to something different?
>>
>> Andrew Marshall
>> PhD Candidate
>> Laboratory of Protein Crystallography
>> Dept. of Molecular and Cellular Biology
>> School of Biological Sciences
>> The University of Adelaide
>>
>> On Tue, Dec 20, 2016 at 1:28 PM, Pavel Afonine 
>> wrote:
>>
>>> Hi Andrew,
>>>
>>> you can define a weak bond between clashing atoms which will disable
>>> repulsion. A weak bond should not introduce any bias.
>>>
>>> Pavel
>>>
>>> On Sun, Dec 18, 2016 at 9:39 PM, Andrew Marshall <
>>> andrew.c.marsh...@adelaide.edu.au> wrote:
>>>
 Hi all,

 I have a structure of a condensing enzyme with substrate bound. The
 active site is very tight, requiring some of the substrate atoms to clash
 with a catalytic cysteine. This means that although the substrate fits the
 density nicely upon manual real-space refinement, phenix recognises the
 clash, resulting in the displacement of substrate atoms so that they are
 outside the density. I can mostly fix this by using distance restraints,
 but I'd rather allow it to refine in a less biased manner, but ignore the
 clash. Is this a acceptable way forward? If so, is there a parameter I can
 edit to tell phenix to ignore clashes between these specific atoms?

 Thanks,

 Andrew Marshall
 PhD Candidate
 Laboratory of Protein Crystallography
 Dept. of Molecular and Cellular Biology
 School of Biological Sciences
 The University of Adelaide


>>>
>>
>

Re: [ccp4bb] Atom clashes in active site?

[Scott Horowitz]

Hi Andrew,

Based on the atoms and distances you are mentioning, these don't sound like
steric clashes, but like a chalcogen bond between the S and O atoms, and
CH...O hydrogen bonds between the O and CH3. These are common and
well-accepted interactions, but unfortunately aren't usually treated as
such by refinement programs. Let me know if you want references for these
interaction types.

Scott

On Mon, Dec 19, 2016 at 8:48 PM, Andrew Marshall <
andrew.c.marsh...@adelaide.edu.au> wrote:

> Hi all,
>
> Thank you for your suggestions. I tried the pdb file edit (making the
> offending atoms of both the ligand and the protein 'B' altconf), but it
> didn't seem to make any difference to their positions after a single round
> of refinement..?
> The atoms in the active site concern two acetyl groups - one from the
> substrate, acetyl-CoA, and the other from an acetylated cysteine in the
> protein - that I believe are poised ready for a condensation reaction. The
> closest contacts are between S and O(carbonyl) atoms (2.9A) and O and CH3
> (3.1A), but going off the density, I think these should be closer (more
> like 2.8 or 2.7A). It may be that I've trapped another reaction
> intermediate (which would be cool), but I don't think that fits the density
> quite as well. Any thoughts/ideas?
>
> Thanks,
>
> Andrew Marshall
> PhD Candidate
> Laboratory of Protein Crystallography
> Dept. of Molecular and Cellular Biology
> School of Biological Sciences
> The University of Adelaide
>
> On Tue, Dec 20, 2016 at 12:09 AM, Scott Horowitz 
> wrote:
>
>> Hi Andrew,
>>
>> I'm curious- what are the atoms that are clashing? I worked on this sort
>> of thing back in my Ph.D., and so I might have some useful tidbits if, for
>> example, the S is clashing with a carbon of some sort.
>>
>> Thanks,
>> Scott
>>
>> On Mon, Dec 19, 2016 at 12:39 AM, Andrew Marshall <
>> andrew.c.marsh...@adelaide.edu.au> wrote:
>>
>>> Hi all,
>>>
>>> I have a structure of a condensing enzyme with substrate bound. The
>>> active site is very tight, requiring some of the substrate atoms to clash
>>> with a catalytic cysteine. This means that although the substrate fits the
>>> density nicely upon manual real-space refinement, phenix recognises the
>>> clash, resulting in the displacement of substrate atoms so that they are
>>> outside the density. I can mostly fix this by using distance restraints,
>>> but I'd rather allow it to refine in a less biased manner, but ignore the
>>> clash. Is this a acceptable way forward? If so, is there a parameter I can
>>> edit to tell phenix to ignore clashes between these specific atoms?
>>>
>>> Thanks,
>>>
>>> Andrew Marshall
>>> PhD Candidate
>>> Laboratory of Protein Crystallography
>>> Dept. of Molecular and Cellular Biology
>>> School of Biological Sciences
>>> The University of Adelaide
>>>
>>>
>>
>>
>> --
>> Scott Horowitz, Ph.D.
>> Postdoctoral Fellow
>>
>> University of Michigan
>> Department of Molecular, Cellular, and Developmental Biology
>> Bardwell lab
>> 830 N. University Ave, Room 4007
>> Ann Arbor, MI 48109
>> phone: 734-647-6683
>> fax: 734-615-4226
>>
>
>


-- 
Scott Horowitz, Ph.D.
Postdoctoral Fellow

University of Michigan
Department of Molecular, Cellular, and Developmental Biology
Bardwell lab
830 N. University Ave, Room 4007
Ann Arbor, MI 48109
phone: 734-647-6683
fax: 734-615-4226

Re: [ccp4bb] Atom clashes in active site?

[Pavel Afonine]

Hi Pedro,

quick answer: no.

Longer answer:
see article "13 typical occupancy refinement scenarios and available
options in phenix.refine" here:
http://phenix-online.org/newsletter/

Pavel

On Tue, Dec 20, 2016 at 12:29 AM, Pedro Matias  wrote:

> Hi Pavel,
>
> If the occupancies are 1 does phenix still refine them? Anyway, they can
> be explicitly fixed if necessary.
>
> Pedro
>
> Às 03:00 de 20/12/2016, Pavel Afonine escreveu:
>
> Hi Perdo,
>
> technically this should work too with the caveat that non-blanc altid will
> trigger occupancy refinement for corresponding atoms which may not be
> desired.
>
> Pavel
>
>
> On Mon, Dec 19, 2016 at 12:54 AM, Pedro Matias  wrote:
>
>> Hi Andrew,
>>
>> The simplest way would be to place the "offending" atoms in separate
>> conformers as used to refine alternate conformations. This is a 1-letter
>> code that goes just before the 3-letter residue name:
>>
>> ATOM139  SG *B*CYS A  21 -20.620   4.518  34.501  0.39
>> 12.23  AS
>>
>> This trick should cause PHENIX to ignore close distances between atoms in
>> the A and B conformers.
>>
>> Hope this helps,
>>
>> Pedro Matias
>>
>>
>> Às 05:39 de 19/12/2016, Andrew Marshall escreveu:
>>
>> Hi all,
>>
>> I have a structure of a condensing enzyme with substrate bound. The
>> active site is very tight, requiring some of the substrate atoms to clash
>> with a catalytic cysteine. This means that although the substrate fits the
>> density nicely upon manual real-space refinement, phenix recognises the
>> clash, resulting in the displacement of substrate atoms so that they are
>> outside the density. I can mostly fix this by using distance restraints,
>> but I'd rather allow it to refine in a less biased manner, but ignore the
>> clash. Is this a acceptable way forward? If so, is there a parameter I can
>> edit to tell phenix to ignore clashes between these specific atoms?
>>
>> Thanks,
>>
>>

Re: [ccp4bb] Atom clashes in active site?

[Pedro Matias]

Hi Andrew,

One of the atoms should be in altconf A and the other in B. Otherwise
the problem remains.

Pedro


Às 01:48 de 20/12/2016, Andrew Marshall escreveu:
> Hi all,
>
> Thank you for your suggestions. I tried the pdb file edit (making the
> offending atoms of both the ligand and the protein 'B' altconf), but
> it didn't seem to make any difference to their positions after a
> single round of refinement..? 
> The atoms in the active site concern two acetyl groups - one from the
> substrate, acetyl-CoA, and the other from an acetylated cysteine in
> the protein - that I believe are poised ready for a condensation
> reaction. The closest contacts are between S and O(carbonyl) atoms
> (2.9A) and O and CH3 (3.1A), but going off the density, I think these
> should be closer (more like 2.8 or 2.7A). It may be that I've trapped
> another reaction intermediate (which would be cool), but I don't think
> that fits the density quite as well. Any thoughts/ideas?
>
> Thanks,
>
> Andrew Marshall
> PhD Candidate
> Laboratory of Protein Crystallography
> Dept. of Molecular and Cellular Biology
> School of Biological Sciences
> The University of Adelaide
>
> On Tue, Dec 20, 2016 at 12:09 AM, Scott Horowitz  > wrote:
>
> Hi Andrew,
>
> I'm curious- what are the atoms that are clashing? I worked on
> this sort of thing back in my Ph.D., and so I might have some
> useful tidbits if, for example, the S is clashing with a carbon of
> some sort.
>
> Thanks,
> Scott
>
> On Mon, Dec 19, 2016 at 12:39 AM, Andrew Marshall
>  > wrote:
>
> Hi all,
>
> I have a structure of a condensing enzyme with substrate
> bound. The active site is very tight, requiring some of the
> substrate atoms to clash with a catalytic cysteine. This means
> that although the substrate fits the density nicely upon
> manual real-space refinement, phenix recognises the clash,
> resulting in the displacement of substrate atoms so that they
> are outside the density. I can mostly fix this by using
> distance restraints, but I'd rather allow it to refine in a
> less biased manner, but ignore the clash. Is this a acceptable
> way forward? If so, is there a parameter I can edit to tell
> phenix to ignore clashes between these specific atoms?
>
> Thanks,
>
> Andrew Marshall
> PhD Candidate
> Laboratory of Protein Crystallography
> Dept. of Molecular and Cellular Biology
> School of Biological Sciences
> The University of Adelaide
>
>
>
>
> -- 
> Scott Horowitz, Ph.D.
> Postdoctoral Fellow
>
> University of Michigan
> Department of Molecular, Cellular, and Developmental Biology
> Bardwell lab
> 830 N. University Ave, Room 4007
> Ann Arbor, MI 48109
> phone: 734-647-6683
> fax: 734-615-4226
>
>

-- 

Industry and Medicine Applied Crystallography
Macromolecular Crystallography Unit
___
Phones : (351-21) 446-9100 Ext. 1669
 (351-21) 446-9669 (direct)
 Fax   : (351-21) 441-1277 or 443-3644

email : mat...@itqb.unl.pt

http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallography
http://www.itqb.unl.pt/labs/macromolecular-crystallography-unit

Mailing address :
Instituto de Tecnologia Quimica e Biologica António Xavier
Universidade Nova de Lisboa
Av. da República
2780-157 Oeiras
PORTUGAL

ITQB NOVA, a great choice for your PhD
https://youtu.be/de6j-aaTWNQ

Master Programme in Biochemistry for Health
https://youtu.be/UKstDCFjYI8

Re: [ccp4bb] Atom clashes in active site?

[Pedro Matias]

Hi Pavel,

If the occupancies are 1 does phenix still refine them? Anyway, they can
be explicitly fixed if necessary.

Pedro


Às 03:00 de 20/12/2016, Pavel Afonine escreveu:
> Hi Perdo,
>
> technically this should work too with the caveat that non-blanc altid
> will trigger occupancy refinement for corresponding atoms which may
> not be desired.
>
> Pavel
>
>
> On Mon, Dec 19, 2016 at 12:54 AM, Pedro Matias  > wrote:
>
> Hi Andrew,
>
> The simplest way would be to place the "offending" atoms in
> separate conformers as used to refine alternate conformations.
> This is a 1-letter code that goes just before the 3-letter residue
> name:
>
>> ATOM139  SG *B*CYS A  21 -20.620   4.518  34.501  0.39
>> 12.23  AS  
> This trick should cause PHENIX to ignore close distances between
> atoms in the A and B conformers.
>
> Hope this helps,
>
> Pedro Matias
>
>
> Às 05:39 de 19/12/2016, Andrew Marshall escreveu:
>> Hi all,
>>
>> I have a structure of a condensing enzyme with substrate bound.
>> The active site is very tight, requiring some of the substrate
>> atoms to clash with a catalytic cysteine. This means that
>> although the substrate fits the density nicely upon manual
>> real-space refinement, phenix recognises the clash, resulting in
>> the displacement of substrate atoms so that they are outside the
>> density. I can mostly fix this by using distance restraints, but
>> I'd rather allow it to refine in a less biased manner, but ignore
>> the clash. Is this a acceptable way forward? If so, is there a
>> parameter I can edit to tell phenix to ignore clashes between
>> these specific atoms?
>>
>> Thanks,
>>
>> Andrew Marshall
>> PhD Candidate
>> Laboratory of Protein Crystallography
>> Dept. of Molecular and Cellular Biology
>> School of Biological Sciences
>> The University of Adelaide
>>
>
> -- 
>
> Industry and Medicine Applied Crystallography
> Macromolecular Crystallography Unit
> ___
> Phones : (351-21) 446-9100 Ext. 1669
>  (351-21) 446-9669 (direct)
>  Fax   : (351-21) 441-1277 or 443-3644
>
> email : mat...@itqb.unl.pt 
>
> 
> http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallography
> 
> 
> http://www.itqb.unl.pt/labs/macromolecular-crystallography-unit
> 
>
> Mailing address :
> Instituto de Tecnologia Quimica e Biologica António Xavier
> Universidade Nova de Lisboa
> Av. da República
> 2780-157 Oeiras
> PORTUGAL
>
> ITQB NOVA, a great choice for your PhD
> https://youtu.be/de6j-aaTWNQ
>
> Master Programme in Biochemistry for Health
> https://youtu.be/UKstDCFjYI8
>
-- 

Industry and Medicine Applied Crystallography
Macromolecular Crystallography Unit
___
Phones : (351-21) 446-9100 Ext. 1669
 (351-21) 446-9669 (direct)
 Fax   : (351-21) 441-1277 or 443-3644

email : mat...@itqb.unl.pt

http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallography
http://www.itqb.unl.pt/labs/macromolecular-crystallography-unit

Mailing address :
Instituto de Tecnologia Quimica e Biologica António Xavier
Universidade Nova de Lisboa
Av. da República
2780-157 Oeiras
PORTUGAL

ITQB NOVA, a great choice for your PhD
https://youtu.be/de6j-aaTWNQ

Master Programme in Biochemistry for Health
https://youtu.be/UKstDCFjYI8

Re: [ccp4bb] Atom clashes in active site?

[Pavel Afonine]

Hi Andrew,

yes, exactly as you describe: set distance_ideal to a meaningful value
(approx. distance between density peaks, doesn't have to be very accurate),
and set sigma to some large number, say 1 or so.

Pavel

On Mon, Dec 19, 2016 at 7:40 PM, Andrew Marshall <
andrew.c.marsh...@adelaide.edu.au> wrote:

> Hi Pavel,
>
> To define a weak bond, would you use "geometry_restraints.edits { ... bond
> {... " , and just set a rough distance_ideal and a very high sigma (like
> say 5A)?
> Or are you referring to something different?
>
> Andrew Marshall
> PhD Candidate
> Laboratory of Protein Crystallography
> Dept. of Molecular and Cellular Biology
> School of Biological Sciences
> The University of Adelaide
>
> On Tue, Dec 20, 2016 at 1:28 PM, Pavel Afonine  wrote:
>
>> Hi Andrew,
>>
>> you can define a weak bond between clashing atoms which will disable
>> repulsion. A weak bond should not introduce any bias.
>>
>> Pavel
>>
>> On Sun, Dec 18, 2016 at 9:39 PM, Andrew Marshall <
>> andrew.c.marsh...@adelaide.edu.au> wrote:
>>
>>> Hi all,
>>>
>>> I have a structure of a condensing enzyme with substrate bound. The
>>> active site is very tight, requiring some of the substrate atoms to clash
>>> with a catalytic cysteine. This means that although the substrate fits the
>>> density nicely upon manual real-space refinement, phenix recognises the
>>> clash, resulting in the displacement of substrate atoms so that they are
>>> outside the density. I can mostly fix this by using distance restraints,
>>> but I'd rather allow it to refine in a less biased manner, but ignore the
>>> clash. Is this a acceptable way forward? If so, is there a parameter I can
>>> edit to tell phenix to ignore clashes between these specific atoms?
>>>
>>> Thanks,
>>>
>>> Andrew Marshall
>>> PhD Candidate
>>> Laboratory of Protein Crystallography
>>> Dept. of Molecular and Cellular Biology
>>> School of Biological Sciences
>>> The University of Adelaide
>>>
>>>
>>
>

Re: [ccp4bb] Atom clashes in active site?

[Andrew Marshall]

Hi Pavel,

To define a weak bond, would you use "geometry_restraints.edits { ... bond
{... " , and just set a rough distance_ideal and a very high sigma (like
say 5A)?
Or are you referring to something different?

Andrew Marshall
PhD Candidate
Laboratory of Protein Crystallography
Dept. of Molecular and Cellular Biology
School of Biological Sciences
The University of Adelaide

On Tue, Dec 20, 2016 at 1:28 PM, Pavel Afonine  wrote:

> Hi Andrew,
>
> you can define a weak bond between clashing atoms which will disable
> repulsion. A weak bond should not introduce any bias.
>
> Pavel
>
> On Sun, Dec 18, 2016 at 9:39 PM, Andrew Marshall <
> andrew.c.marsh...@adelaide.edu.au> wrote:
>
>> Hi all,
>>
>> I have a structure of a condensing enzyme with substrate bound. The
>> active site is very tight, requiring some of the substrate atoms to clash
>> with a catalytic cysteine. This means that although the substrate fits the
>> density nicely upon manual real-space refinement, phenix recognises the
>> clash, resulting in the displacement of substrate atoms so that they are
>> outside the density. I can mostly fix this by using distance restraints,
>> but I'd rather allow it to refine in a less biased manner, but ignore the
>> clash. Is this a acceptable way forward? If so, is there a parameter I can
>> edit to tell phenix to ignore clashes between these specific atoms?
>>
>> Thanks,
>>
>> Andrew Marshall
>> PhD Candidate
>> Laboratory of Protein Crystallography
>> Dept. of Molecular and Cellular Biology
>> School of Biological Sciences
>> The University of Adelaide
>>
>>
>

Re: [ccp4bb] Atom clashes in active site?

[Pavel Afonine]

Hi Perdo,

technically this should work too with the caveat that non-blanc altid will
trigger occupancy refinement for corresponding atoms which may not be
desired.

Pavel


On Mon, Dec 19, 2016 at 12:54 AM, Pedro Matias  wrote:

> Hi Andrew,
>
> The simplest way would be to place the "offending" atoms in separate
> conformers as used to refine alternate conformations. This is a 1-letter
> code that goes just before the 3-letter residue name:
>
> ATOM139  SG *B*CYS A  21 -20.620   4.518  34.501  0.39 12.23
> AS
>
> This trick should cause PHENIX to ignore close distances between atoms in
> the A and B conformers.
>
> Hope this helps,
>
> Pedro Matias
>
>
> Às 05:39 de 19/12/2016, Andrew Marshall escreveu:
>
> Hi all,
>
> I have a structure of a condensing enzyme with substrate bound. The active
> site is very tight, requiring some of the substrate atoms to clash with a
> catalytic cysteine. This means that although the substrate fits the density
> nicely upon manual real-space refinement, phenix recognises the clash,
> resulting in the displacement of substrate atoms so that they are outside
> the density. I can mostly fix this by using distance restraints, but I'd
> rather allow it to refine in a less biased manner, but ignore the clash. Is
> this a acceptable way forward? If so, is there a parameter I can edit to
> tell phenix to ignore clashes between these specific atoms?
>
> Thanks,
>
> Andrew Marshall
> PhD Candidate
> Laboratory of Protein Crystallography
> Dept. of Molecular and Cellular Biology
> School of Biological Sciences
> The University of Adelaide
>
>
> --
>
> Industry and Medicine Applied Crystallography
> Macromolecular Crystallography Unit
> ___
> Phones : (351-21) 446-9100 Ext. 1669
>  (351-21) 446-9669 (direct)
>  Fax   : (351-21) 441-1277 or 443-3644
>
> email : mat...@itqb.unl.pt
> http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallographyhttp://www.itqb.unl.pt/labs/macromolecular-crystallography-unit
>
> Mailing address :
> Instituto de Tecnologia Quimica e Biologica António Xavier
> Universidade Nova de Lisboa
> Av. da República
> 2780-157 Oeiras
> PORTUGAL
>
> ITQB NOVA, a great choice for your PhDhttps://youtu.be/de6j-aaTWNQ
>
> Master Programme in Biochemistry for Healthhttps://youtu.be/UKstDCFjYI8
>
>

Re: [ccp4bb] Atom clashes in active site?

[Pavel Afonine]

Hi Andrew,

you can define a weak bond between clashing atoms which will disable
repulsion. A weak bond should not introduce any bias.

Pavel

On Sun, Dec 18, 2016 at 9:39 PM, Andrew Marshall <
andrew.c.marsh...@adelaide.edu.au> wrote:

> Hi all,
>
> I have a structure of a condensing enzyme with substrate bound. The active
> site is very tight, requiring some of the substrate atoms to clash with a
> catalytic cysteine. This means that although the substrate fits the density
> nicely upon manual real-space refinement, phenix recognises the clash,
> resulting in the displacement of substrate atoms so that they are outside
> the density. I can mostly fix this by using distance restraints, but I'd
> rather allow it to refine in a less biased manner, but ignore the clash. Is
> this a acceptable way forward? If so, is there a parameter I can edit to
> tell phenix to ignore clashes between these specific atoms?
>
> Thanks,
>
> Andrew Marshall
> PhD Candidate
> Laboratory of Protein Crystallography
> Dept. of Molecular and Cellular Biology
> School of Biological Sciences
> The University of Adelaide
>
>

Re: [ccp4bb] Atom clashes in active site?

[Joel Tyndall]

Could this be a covalent interaction?

Difficult to judge without seeing anything

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Andrew 
Marshall
Sent: Tuesday, 20 December 2016 2:48 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Atom clashes in active site?

Hi all,

Thank you for your suggestions. I tried the pdb file edit (making the offending 
atoms of both the ligand and the protein 'B' altconf), but it didn't seem to 
make any difference to their positions after a single round of refinement..?
The atoms in the active site concern two acetyl groups - one from the 
substrate, acetyl-CoA, and the other from an acetylated cysteine in the protein 
- that I believe are poised ready for a condensation reaction. The closest 
contacts are between S and O(carbonyl) atoms (2.9A) and O and CH3 (3.1A), but 
going off the density, I think these should be closer (more like 2.8 or 2.7A). 
It may be that I've trapped another reaction intermediate (which would be 
cool), but I don't think that fits the density quite as well. Any 
thoughts/ideas?

Thanks,

Andrew Marshall
PhD Candidate
Laboratory of Protein Crystallography
Dept. of Molecular and Cellular Biology
School of Biological Sciences
The University of Adelaide

On Tue, Dec 20, 2016 at 12:09 AM, Scott Horowitz 
<horow...@umich.edu<mailto:horow...@umich.edu>> wrote:
Hi Andrew,
I'm curious- what are the atoms that are clashing? I worked on this sort of 
thing back in my Ph.D., and so I might have some useful tidbits if, for 
example, the S is clashing with a carbon of some sort.
Thanks,
Scott

On Mon, Dec 19, 2016 at 12:39 AM, Andrew Marshall 
<andrew.c.marsh...@adelaide.edu.au<mailto:andrew.c.marsh...@adelaide.edu.au>> 
wrote:
Hi all,

I have a structure of a condensing enzyme with substrate bound. The active site 
is very tight, requiring some of the substrate atoms to clash with a catalytic 
cysteine. This means that although the substrate fits the density nicely upon 
manual real-space refinement, phenix recognises the clash, resulting in the 
displacement of substrate atoms so that they are outside the density. I can 
mostly fix this by using distance restraints, but I'd rather allow it to refine 
in a less biased manner, but ignore the clash. Is this a acceptable way 
forward? If so, is there a parameter I can edit to tell phenix to ignore 
clashes between these specific atoms?

Thanks,

Andrew Marshall
PhD Candidate
Laboratory of Protein Crystallography
Dept. of Molecular and Cellular Biology
School of Biological Sciences
The University of Adelaide



--
Scott Horowitz, Ph.D.
Postdoctoral Fellow

University of Michigan
Department of Molecular, Cellular, and Developmental Biology
Bardwell lab
830 N. University Ave, Room 4007
Ann Arbor, MI 48109
phone: 734-647-6683
fax: 734-615-4226

Re: [ccp4bb] Atom clashes in active site?

[Andrew Marshall]

Hi all,

Thank you for your suggestions. I tried the pdb file edit (making the
offending atoms of both the ligand and the protein 'B' altconf), but it
didn't seem to make any difference to their positions after a single round
of refinement..?
The atoms in the active site concern two acetyl groups - one from the
substrate, acetyl-CoA, and the other from an acetylated cysteine in the
protein - that I believe are poised ready for a condensation reaction. The
closest contacts are between S and O(carbonyl) atoms (2.9A) and O and CH3
(3.1A), but going off the density, I think these should be closer (more
like 2.8 or 2.7A). It may be that I've trapped another reaction
intermediate (which would be cool), but I don't think that fits the density
quite as well. Any thoughts/ideas?

Thanks,

Andrew Marshall
PhD Candidate
Laboratory of Protein Crystallography
Dept. of Molecular and Cellular Biology
School of Biological Sciences
The University of Adelaide

On Tue, Dec 20, 2016 at 12:09 AM, Scott Horowitz  wrote:

> Hi Andrew,
>
> I'm curious- what are the atoms that are clashing? I worked on this sort
> of thing back in my Ph.D., and so I might have some useful tidbits if, for
> example, the S is clashing with a carbon of some sort.
>
> Thanks,
> Scott
>
> On Mon, Dec 19, 2016 at 12:39 AM, Andrew Marshall <
> andrew.c.marsh...@adelaide.edu.au> wrote:
>
>> Hi all,
>>
>> I have a structure of a condensing enzyme with substrate bound. The
>> active site is very tight, requiring some of the substrate atoms to clash
>> with a catalytic cysteine. This means that although the substrate fits the
>> density nicely upon manual real-space refinement, phenix recognises the
>> clash, resulting in the displacement of substrate atoms so that they are
>> outside the density. I can mostly fix this by using distance restraints,
>> but I'd rather allow it to refine in a less biased manner, but ignore the
>> clash. Is this a acceptable way forward? If so, is there a parameter I can
>> edit to tell phenix to ignore clashes between these specific atoms?
>>
>> Thanks,
>>
>> Andrew Marshall
>> PhD Candidate
>> Laboratory of Protein Crystallography
>> Dept. of Molecular and Cellular Biology
>> School of Biological Sciences
>> The University of Adelaide
>>
>>
>
>
> --
> Scott Horowitz, Ph.D.
> Postdoctoral Fellow
>
> University of Michigan
> Department of Molecular, Cellular, and Developmental Biology
> Bardwell lab
> 830 N. University Ave, Room 4007
> Ann Arbor, MI 48109
> phone: 734-647-6683
> fax: 734-615-4226
>

Re: [ccp4bb] Atom clashes in active site?

[Pedro Matias]

Hi Andrew,

The simplest way would be to place the "offending" atoms in separate
conformers as used to refine alternate conformations. This is a 1-letter
code that goes just before the 3-letter residue name:

> ATOM139  SG *B*CYS A  21 -20.620   4.518  34.501  0.39
> 12.23  AS  
This trick should cause PHENIX to ignore close distances between atoms
in the A and B conformers.

Hope this helps,

Pedro Matias


Às 05:39 de 19/12/2016, Andrew Marshall escreveu:
> Hi all,
>
> I have a structure of a condensing enzyme with substrate bound. The
> active site is very tight, requiring some of the substrate atoms to
> clash with a catalytic cysteine. This means that although the
> substrate fits the density nicely upon manual real-space refinement,
> phenix recognises the clash, resulting in the displacement of
> substrate atoms so that they are outside the density. I can mostly fix
> this by using distance restraints, but I'd rather allow it to refine
> in a less biased manner, but ignore the clash. Is this a acceptable
> way forward? If so, is there a parameter I can edit to tell phenix to
> ignore clashes between these specific atoms?
>
> Thanks,
>
> Andrew Marshall
> PhD Candidate
> Laboratory of Protein Crystallography
> Dept. of Molecular and Cellular Biology
> School of Biological Sciences
> The University of Adelaide
>

-- 

Industry and Medicine Applied Crystallography
Macromolecular Crystallography Unit
___
Phones : (351-21) 446-9100 Ext. 1669
 (351-21) 446-9669 (direct)
 Fax   : (351-21) 441-1277 or 443-3644

email : mat...@itqb.unl.pt

http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallography
http://www.itqb.unl.pt/labs/macromolecular-crystallography-unit

Mailing address :
Instituto de Tecnologia Quimica e Biologica António Xavier
Universidade Nova de Lisboa
Av. da República
2780-157 Oeiras
PORTUGAL

ITQB NOVA, a great choice for your PhD
https://youtu.be/de6j-aaTWNQ

Master Programme in Biochemistry for Health
https://youtu.be/UKstDCFjYI8