Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] Modeling ATP/ADP

2020-07-24 Thread Oleg Kovalevskiy - UKRI STFC 

Dear Reza,

We had a case when two phosphate ions and magnesium ion have been bound to the 
ATP-binding site (300mM sodium phosphate in the crystallisations conditions). 
However, your ATP/ADP may not have full occupancy and therefore electron 
density might be lower. You may consider calculation of a blurred map (bring up 
contributions from low-resolution terms) and see whether there is any density 
for the nucleotide.
But first of all I would calculate omit map (without ligand) and would start to 
worry if there is no density for nucleotide part.

All the best,
Oleg

--
Dr Oleg Kovalevskiy
CCP4 team
UKRI Science and Technology Facilities Council
Rutherford Appleton Laboratory
Harwell Campus
Didcot, Oxfordshire
OX11 0QX
UK

From: CCP4 bulletin board  on behalf of Reza Khayat 

Reply to: Reza Khayat 
Date: Thursday, 23 July 2020 at 21:13
To: ccp4bb 
Subject: Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] Modeling ATP/ADP


Tried the homologues thing. There are homologues and I've done the fitting, but 
this is what I consider to be subjective. I'm certain the referee will ask: 
Given the quality of density for the nucleotide, how certain are the authors 
that a different fit is not possible? Have other fit poses been considered?



Reza


Reza Khayat, PhD
Assistant Professor
City College of New York
Department of Chemistry and Biochemistry
New York, NY 10031

From: CCP4 bulletin board  on behalf of Jon Cooper 
<488a26d62010-dmarc-requ...@jiscmail.ac.uk>
Sent: Thursday, July 23, 2020 1:07 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [EXTERNAL] Re: [ccp4bb] Modeling ATP/ADP

Hello, do you have any homologues in the PDB with ATP, etc, bound as a guide? 
Coot is pretty good at fitting known ligands, and unknown ones, too!


 Original Message 
On 23 Jul 2020, 17:53, Reza Khayat < rkha...@ccny.cuny.edu> wrote:


Hi,



Can folks suggest programs for objectively docking ATP/ADP molecules into 
density? Our density is not so good, probably because of occupancy, and we'd 
like a less subjecting approach for modeling. Thanks.



Best wishes,
Reza


Reza Khayat, PhD
Assistant Professor
City College of New York
Department of Chemistry and Biochemistry
New York, NY 10031



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Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] Modeling ATP/ADP

2020-07-23 Thread LMB 

... and don’t forget the Mg++ ion

Sent from my iPad

> On 23 Jul 2020, at 20:10, LMB  wrote:
> 
> One way of approaching such modelling uncertainties is to build explicitly a 
> number of likely models, refine them and examine the difference maps 
> carefully to see whether you can convince yourself that one model is clearly 
> better than the others. At least then you will know whether the alternatives 
> are distinguishable 
> Phil
> 
> Sent from my iPad
> 
>>> On 23 Jul 2020, at 18:12, Reza Khayat  wrote:
>>> 
>> 
>> Tried the homologues thing. There are homologues and I've done the fitting, 
>> but this is what I consider to be subjective. I'm certain the referee will 
>> ask: Given the quality of density for the nucleotide, how certain are the 
>> authors that a different fit is not possible? Have other fit poses been 
>> considered?
>> 
>> 
>> 
>> Reza
>> 
>> 
>> 
>> Reza Khayat, PhD
>> Assistant Professor 
>> City College of New York
>> Department of Chemistry and Biochemistry
>> New York, NY 10031
>> From: CCP4 bulletin board  on behalf of Jon Cooper 
>> <488a26d62010-dmarc-requ...@jiscmail.ac.uk>
>> Sent: Thursday, July 23, 2020 1:07 PM
>> To: CCP4BB@JISCMAIL.AC.UK
>> Subject: [EXTERNAL] Re: [ccp4bb] Modeling ATP/ADP
>>  
>> Hello, do you have any homologues in the PDB with ATP, etc, bound as a 
>> guide? Coot is pretty good at fitting known ligands, and unknown ones, too!
>> 
>> 
>>  Original Message 
>> On 23 Jul 2020, 17:53, Reza Khayat < rkha...@ccny.cuny.edu> wrote:
>> 
>> Hi,
>> 
>> 
>> 
>> Can folks suggest programs for objectively docking ATP/ADP molecules into 
>> density? Our density is not so good, probably because of occupancy, and we'd 
>> like a less subjecting approach for modeling. Thanks.
>> 
>> 
>> 
>> Best wishes,
>> Reza
>> 
>> 
>> 
>> Reza Khayat, PhD
>> Assistant Professor 
>> City College of New York
>> Department of Chemistry and Biochemistry
>> New York, NY 10031
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>> 
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
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>> 
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Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] Modeling ATP/ADP

2020-07-23 Thread LMB 
One way of approaching such modelling uncertainties is to build explicitly a 
number of likely models, refine them and examine the difference maps carefully 
to see whether you can convince yourself that one model is clearly better than 
the others. At least then you will know whether the alternatives are 
distinguishable 
Phil

Sent from my iPad

> On 23 Jul 2020, at 18:12, Reza Khayat  wrote:
> 
> 
> Tried the homologues thing. There are homologues and I've done the fitting, 
> but this is what I consider to be subjective. I'm certain the referee will 
> ask: Given the quality of density for the nucleotide, how certain are the 
> authors that a different fit is not possible? Have other fit poses been 
> considered?
> 
> 
> 
> Reza
> 
> 
> 
> Reza Khayat, PhD
> Assistant Professor 
> City College of New York
> Department of Chemistry and Biochemistry
> New York, NY 10031
> From: CCP4 bulletin board  on behalf of Jon Cooper 
> <488a26d62010-dmarc-requ...@jiscmail.ac.uk>
> Sent: Thursday, July 23, 2020 1:07 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [EXTERNAL] Re: [ccp4bb] Modeling ATP/ADP
>  
> Hello, do you have any homologues in the PDB with ATP, etc, bound as a guide? 
> Coot is pretty good at fitting known ligands, and unknown ones, too!
> 
> 
>  Original Message 
> On 23 Jul 2020, 17:53, Reza Khayat < rkha...@ccny.cuny.edu> wrote:
> 
> Hi,
> 
> 
> 
> Can folks suggest programs for objectively docking ATP/ADP molecules into 
> density? Our density is not so good, probably because of occupancy, and we'd 
> like a less subjecting approach for modeling. Thanks.
> 
> 
> 
> Best wishes,
> Reza
> 
> 
> 
> Reza Khayat, PhD
> Assistant Professor 
> City College of New York
> Department of Chemistry and Biochemistry
> New York, NY 10031
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> 
> 
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Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] Modeling ATP/ADP

2020-07-23 Thread Andrew Leslie 
Dear Reza,

  I would back Jon’s idea of looking at homologues, although 
this does depend on how close the homologue is. For example, if your protein 
has a “P” loop, with the Walker A sequence motif, then I think it would be very 
surprising if the nucleotide bound in different way to other P loop proteins. 
However, another objective way of fitting is to look at the stereochemical 
environment of the binding site. You might expect the phosphates to have 
several hydrogen bonds to the protein, very possibly involving basic side 
chains (Arg or Lys) and main chain amide groups. The adenine ring, on the other 
hand, typically sits in a more hydrophobic pocket, often with the adenine ring 
involved in a stacking interaction with a side chain.

The other objective test you can do is to try refining with different ways of 
modelling the nucleotide binding and see if the 2FoFc and difference maps look 
better for one binding mode than the others (and if the atomic B factors look 
more sensible). The phosphate groups are significantly more electron dense than 
the rest of the nucleotide. However if the density really is poor, it might be 
difficult to get an unambiguous answer, in which case you might have to rely on 
the stereochemical environment.

Good luck,

Andrew


> On 23 Jul 2020, at 18:12, Reza Khayat  wrote:
> 
> Tried the homologues thing. There are homologues and I've done the fitting, 
> but this is what I consider to be subjective. I'm certain the referee will 
> ask: Given the quality of density for the nucleotide, how certain are the 
> authors that a different fit is not possible? Have other fit poses been 
> considered?
> 
> Reza
> 
> Reza Khayat, PhD
> Assistant Professor 
> City College of New York
> Department of Chemistry and Biochemistry
> New York, NY 10031
> From: CCP4 bulletin board  on behalf of Jon Cooper 
> <488a26d62010-dmarc-requ...@jiscmail.ac.uk>
> Sent: Thursday, July 23, 2020 1:07 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [EXTERNAL] Re: [ccp4bb] Modeling ATP/ADP
>  
> Hello, do you have any homologues in the PDB with ATP, etc, bound as a guide? 
> Coot is pretty good at fitting known ligands, and unknown ones, too!
> 
> 
>  Original Message 
> On 23 Jul 2020, 17:53, Reza Khayat < rkha...@ccny.cuny.edu> wrote:
> 
> Hi,
> 
> Can folks suggest programs for objectively docking ATP/ADP molecules into 
> density? Our density is not so good, probably because of occupancy, and we'd 
> like a less subjecting approach for modeling. Thanks.
> 
> Best wishes,
> Reza
> 
> Reza Khayat, PhD
> Assistant Professor 
> City College of New York
> Department of Chemistry and Biochemistry
> New York, NY 10031
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 
> 
> To unsubscribe from the CCP4BB list, click the following link:
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> 



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Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] Modeling ATP/ADP

2020-07-23 Thread Reza Khayat 
Tried the homologues thing. There are homologues and I've done the fitting, but 
this is what I consider to be subjective. I'm certain the referee will ask: 
Given the quality of density for the nucleotide, how certain are the authors 
that a different fit is not possible? Have other fit poses been considered?


Reza


Reza Khayat, PhD
Assistant Professor
City College of New York
Department of Chemistry and Biochemistry
New York, NY 10031

From: CCP4 bulletin board  on behalf of Jon Cooper 
<488a26d62010-dmarc-requ...@jiscmail.ac.uk>
Sent: Thursday, July 23, 2020 1:07 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [EXTERNAL] Re: [ccp4bb] Modeling ATP/ADP

Hello, do you have any homologues in the PDB with ATP, etc, bound as a guide? 
Coot is pretty good at fitting known ligands, and unknown ones, too!


 Original Message 
On 23 Jul 2020, 17:53, Reza Khayat < rkha...@ccny.cuny.edu> wrote:


Hi,


Can folks suggest programs for objectively docking ATP/ADP molecules into 
density? Our density is not so good, probably because of occupancy, and we'd 
like a less subjecting approach for modeling. Thanks.


Best wishes,
Reza


Reza Khayat, PhD
Assistant Professor
City College of New York
Department of Chemistry and Biochemistry
New York, NY 10031



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