Re: [ccp4bb] Help with interpreting Tyrosine modification

[Jon Cooper]

Hello, yes, that's right. We've all seen guanidinium groups parallel with 
aromatic rings and shielding them from solvent. I think it might approach that 
sort of arrangement in this case. Cheers, Jon.C.

Sent from ProtonMail mobile

 Original Message 
On 1 Feb 2022, 16:52, Krieger, James M wrote:

> Probably arginine and tyrosine do like each other a fair bit. They can form 
> both cation-pi interactions and hydrogen bonds.
> Best wishes
> James
>
>> On 1 Feb 2022, at 16:41, Jon Cooper 
>> <488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>> Hello, I did wonder if it might be an alternative conformation for the 
>> quanidinium group of that nearby arginine. Being such high resolution, quite 
>> low occupancy groups would show up, I think, but it may just be too far away 
>> and I don't know how much tyrosine and arginine like each other!
>>
>> Sent from ProtonMail mobile
>>
>>  Original Message 
>> On 1 Feb 2022, 09:28, Misba Ahmad < misba.ah...@gmail.com> wrote:
>>
>>> Thank you for your suggestions.
>>> As this is a high resolution structure (1.1Å) I have been refining it with 
>>> anisotropic B-factors.
>>> Placing a propionate or modelling a phosphate at this position blows up 
>>> during the refinement.
>>> I will inform you if I am successful in figuring this out.
>>>
>>> Best
>>> Misbha
>>>
>>> On Sat, Jan 29, 2022 at 7:01 PM SHEPARD William 
>>>  wrote:
>>>
 Dear Misba,

 Perhaps it's a silly question, but have you tried to model in propionate? 
 The carboxylate group could make H-bonds to both the Arginine sidechain 
 and the the tyrosine OH group. Propionate should show no anomalous signal.

 Just my 2-bits worth.

 Cheers,
 Bill

 - Original Message -
 From: "Gerard Bricogne" 
 To: CCP4BB@JISCMAIL.AC.UK
 Sent: Saturday, 29 January, 2022 18:34:26
 Subject: Re: [ccp4bb] Help with interpreting Tyrosine modification

 Dear Misba,

 Thank you for your reply and for the very clear picture. I hope you
 will be able to share the result once the mystery is solved.

 With best wishes,

 Gerard.

 --
 On Sat, Jan 29, 2022 at 03:32:30PM +0100, Misba Ahmad wrote:
> Dear Gerard,
> The data were collected at 0.966Å and I can see the anomalous peaks for As
> at Cysteines which are modified and I have correctly modelled those (see
> image below). However, at this Tyr, I don't see an anomalous signal.
>
> [image: 4.png]
>
> On Sat, Jan 29, 2022 at 3:06 PM Gerard Bricogne 
> wrote:
>
> > Dear Misba,
> >
> > A wild guess: have you considered the possibility that this extra
> > density could be a cacodylate adduct? Cacodylate is well known to react
> > with
> > thiols - see
> >
> >
> > [https://febs.onlinelibrary.wiley.com/doi/pdfdirect/10.1016/0014-5793(72)80224-2](https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Ffebs.onlinelibrary.wiley.com%2Fdoi%2Fpdfdirect%2F10.1016%2F0014-5793(72)80224-2=04%7C01%7Ckriegerj%40PITT.EDU%7C3bfe6a715d964db88a1c08d9e5a1740e%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637793305180888406%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000=quySIsk%2BnzbHh5o3bYoOGbiXsx1ItJGTt3y6aI2oc5M%3D=0)
> >
> > Here the chemistry is different but you never know. If your data are
> > redundant enough that you have good anomalous completeness, and were
> > collected above the As K-edge (11.8667 keV), it might be a good idea to
> > compute an anomalous difference Fourier and check for the presence of a
> > peak
> > at the same location as the highest one in your ordinary difference map.
> >
> > Only a wild guess, though ... .
> >
> >
> > With best wishes,
> >
> > Gerard.
> >
> > --
> > On Sat, Jan 29, 2022 at 12:18:58PM +0100, Misba Ahmad wrote:
> > > Placing a water molecule satisfies most of the density and forms nice
> > > H-bonds but there is still some residual density left (8.6 and 5.6 
> > > rmsd).
> > >
> > > Best
> > > Misbha
> > > [image: 3.png]
> > >
> > >
> > > On Sat, Jan 29, 2022 at 11:05 AM Klaus Futterer 
> > > 
> > > wrote:
> > >
> > > > Looks more like water molecules. Phosphorylation would give a much
> > bigger
> > > > peak, and shape of density does not fit either. I don't think this 
> > > > is a
> > > > covalent modification. Model some water molecules and see what the
> > > > distances are and what difference density is left.
> > > >
> > > >
> > > > Klaus
> > > >
> > > >
> > > > ===
> > > > Klaus Fütterer, PhD
> > > > Reader in Structural Biology
> > > >
> > > >
> > > > School of Biosciences
> > > > LES College Email:
> > > > 

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E-mail: ols...@uthscsa.edu



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Re: [ccp4bb] Help with interpreting Tyrosine modification

[Krieger, James M]

Probably arginine and tyrosine do like each other a fair bit. They can form 
both cation-pi interactions and hydrogen bonds.
Best wishes
James

On 1 Feb 2022, at 16:41, Jon Cooper 
<488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:

Hello, I did wonder if it might be an alternative conformation for the 
quanidinium group of that nearby arginine. Being such high resolution, quite 
low occupancy groups would show up, I think, but it may just be too far away 
and I don't know how much tyrosine and arginine like each other!


Sent from ProtonMail mobile



 Original Message 
On 1 Feb 2022, 09:28, Misba Ahmad < misba.ah...@gmail.com> wrote:

Thank you for your suggestions.
As this is a high resolution structure (1.1Å) I have been refining it with 
anisotropic B-factors.
Placing a propionate or modelling a phosphate at this position blows up during 
the refinement.
I will inform you if I am successful in figuring this out.

Best
Misbha


On Sat, Jan 29, 2022 at 7:01 PM SHEPARD William 
mailto:william.shep...@synchrotron-soleil.fr>>
 wrote:
Dear Misba,

Perhaps it's a silly question, but have you tried to model in propionate? The 
carboxylate group could make H-bonds to both the Arginine sidechain and the the 
tyrosine OH group. Propionate should show no anomalous signal.

Just my 2-bits worth.

Cheers,
Bill


- Original Message -
From: "Gerard Bricogne" mailto:g...@globalphasing.com>>
To: CCP4BB@JISCMAIL.AC.UK
Sent: Saturday, 29 January, 2022 18:34:26
Subject: Re: [ccp4bb] Help with interpreting Tyrosine modification

Dear Misba,

 Thank you for your reply and for the very clear picture. I hope you
will be able to share the result once the mystery is solved.

 With best wishes,

  Gerard.

--
On Sat, Jan 29, 2022 at 03:32:30PM +0100, Misba Ahmad wrote:
> Dear Gerard,
> The data were collected at 0.966Å and I can see the anomalous peaks for As
> at Cysteines which are modified and I have correctly modelled those (see
> image below). However, at this Tyr, I don't see an anomalous signal.
>
> [image: 4.png]
>
> On Sat, Jan 29, 2022 at 3:06 PM Gerard Bricogne 
> mailto:g...@globalphasing.com>>
> wrote:
>
> > Dear Misba,
> >
> >  A wild guess: have you considered the possibility that this extra
> > density could be a cacodylate adduct? Cacodylate is well known to react
> > with
> > thiols - see
> >
> >
> > https://febs.onlinelibrary.wiley.com/doi/pdfdirect/10.1016/0014-5793(72)80224-2
> >
> > Here the chemistry is different but you never know. If your data are
> > redundant enough that you have good anomalous completeness, and were
> > collected above the As K-edge (11.8667 keV), it might be a good idea to
> > compute an anomalous difference Fourier and check for the presence of a
> > peak
> > at the same location as the highest one in your ordinary difference map.
> >
> >  Only a wild guess, though ... .
> >
> >
> >  With best wishes,
> >
> >   Gerard.
> >
> > --
> > On Sat, Jan 29, 2022 at 12:18:58PM +0100, Misba Ahmad wrote:
> > > Placing a water molecule satisfies most of the density and forms nice
> > > H-bonds but there is still some residual density left (8.6 and 5.6 rmsd).
> > >
> > > Best
> > > Misbha
> > > [image: 3.png]
> > >
> > >
> > > On Sat, Jan 29, 2022 at 11:05 AM Klaus Futterer 
> > > mailto:k.futte...@bham.ac.uk>>
> > > wrote:
> > >
> > > > Looks more like water molecules. Phosphorylation would give a much
> > bigger
> > > > peak, and shape of density does not fit either. I don't think this is a
> > > > covalent modification. Model some water molecules and see what the
> > > > distances are and what difference density is left.
> > > >
> > > >
> > > > Klaus
> > > >
> > > >
> > > > ===
> > > > Klaus Fütterer, PhD
> > > > Reader in Structural Biology
> > > >
> > > >
> > > > School of Biosciences
> > > > LES CollegeEmail:
> > > > k.futte...@bham.ac.uk
> > > > University of Birmingham Phone: +44 - 121 - 414
> > > > 5895
> > > > Birmingham, B15 2TT, UK(voice mail messages
> > > > will forward to my email inbox)
> > > >
> > > > My normal working hours are Mon - Fri 8.30 - 5.30 pm.
> > > >
> > > >
> > > > ===
> > > > --
> > > > *From:* CCP4 bulletin board 
> > > > mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf of
> > > > 

Re: [ccp4bb] Help with interpreting Tyrosine modification

[Jon Cooper]

Hello, I did wonder if it might be an alternative conformation for the 
quanidinium group of that nearby arginine. Being such high resolution, quite 
low occupancy groups would show up, I think, but it may just be too far away 
and I don't know how much tyrosine and arginine like each other!

Sent from ProtonMail mobile

 Original Message 
On 1 Feb 2022, 09:28, Misba Ahmad wrote:

> Thank you for your suggestions.
> As this is a high resolution structure (1.1Å) I have been refining it with 
> anisotropic B-factors.
> Placing a propionate or modelling a phosphate at this position blows up 
> during the refinement.
> I will inform you if I am successful in figuring this out.
>
> Best
> Misbha
>
> On Sat, Jan 29, 2022 at 7:01 PM SHEPARD William 
>  wrote:
>
>> Dear Misba,
>>
>> Perhaps it's a silly question, but have you tried to model in propionate? 
>> The carboxylate group could make H-bonds to both the Arginine sidechain and 
>> the the tyrosine OH group. Propionate should show no anomalous signal.
>>
>> Just my 2-bits worth.
>>
>> Cheers,
>> Bill
>>
>> - Original Message -
>> From: "Gerard Bricogne" 
>> To: CCP4BB@JISCMAIL.AC.UK
>> Sent: Saturday, 29 January, 2022 18:34:26
>> Subject: Re: [ccp4bb] Help with interpreting Tyrosine modification
>>
>> Dear Misba,
>>
>> Thank you for your reply and for the very clear picture. I hope you
>> will be able to share the result once the mystery is solved.
>>
>> With best wishes,
>>
>> Gerard.
>>
>> --
>> On Sat, Jan 29, 2022 at 03:32:30PM +0100, Misba Ahmad wrote:
>>> Dear Gerard,
>>> The data were collected at 0.966Å and I can see the anomalous peaks for As
>>> at Cysteines which are modified and I have correctly modelled those (see
>>> image below). However, at this Tyr, I don't see an anomalous signal.
>>>
>>> [image: 4.png]
>>>
>>> On Sat, Jan 29, 2022 at 3:06 PM Gerard Bricogne 
>>> wrote:
>>>
>>> > Dear Misba,
>>> >
>>> > A wild guess: have you considered the possibility that this extra
>>> > density could be a cacodylate adduct? Cacodylate is well known to react
>>> > with
>>> > thiols - see
>>> >
>>> >
>>> > https://febs.onlinelibrary.wiley.com/doi/pdfdirect/10.1016/0014-5793(72)80224-2
>>> >
>>> > Here the chemistry is different but you never know. If your data are
>>> > redundant enough that you have good anomalous completeness, and were
>>> > collected above the As K-edge (11.8667 keV), it might be a good idea to
>>> > compute an anomalous difference Fourier and check for the presence of a
>>> > peak
>>> > at the same location as the highest one in your ordinary difference map.
>>> >
>>> > Only a wild guess, though ... .
>>> >
>>> >
>>> > With best wishes,
>>> >
>>> > Gerard.
>>> >
>>> > --
>>> > On Sat, Jan 29, 2022 at 12:18:58PM +0100, Misba Ahmad wrote:
>>> > > Placing a water molecule satisfies most of the density and forms nice
>>> > > H-bonds but there is still some residual density left (8.6 and 5.6 
>>> > > rmsd).
>>> > >
>>> > > Best
>>> > > Misbha
>>> > > [image: 3.png]
>>> > >
>>> > >
>>> > > On Sat, Jan 29, 2022 at 11:05 AM Klaus Futterer 
>>> > > wrote:
>>> > >
>>> > > > Looks more like water molecules. Phosphorylation would give a much
>>> > bigger
>>> > > > peak, and shape of density does not fit either. I don't think this is 
>>> > > > a
>>> > > > covalent modification. Model some water molecules and see what the
>>> > > > distances are and what difference density is left.
>>> > > >
>>> > > >
>>> > > > Klaus
>>> > > >
>>> > > >
>>> > > > ===
>>> > > > Klaus Fütterer, PhD
>>> > > > Reader in Structural Biology
>>> > > >
>>> > > >
>>> > > > School of Biosciences
>>> > > > LES College Email:
>>> > > > k.futte...@bham.ac.uk
>>> > > > University of Birmingham Phone: +44 - 121 - 414
>>> > > > 5895
>>> > > > Birmingham, B15 2TT, UK (voice mail messages
>>> > > > will forward to my email inbox)
>>> > > >
>>> > > > My normal working hours are Mon - Fri 8.30 - 5.30 pm.
>>> > > >
>>> > > >
>>> > > > ===
>>> > > > --
>>> > > > *From:* CCP4 bulletin board  on behalf of
>>> > > > misba.ah...@gmail.com 
>>> > > > *Sent:* 29 January 2022 09:45:24
>>> > > > *To:* CCP4BB@JISCMAIL.AC.UK
>>> > > > *Subject:* Re: [ccp4bb] Help with interpreting Tyrosine modification
>>> > > >
>>> > > > Hi Tom,
>>> > > > The protein was expressed in E Coli.
>>> > > >
>>> > > > Best
>>> > > > Misbha
>>> > > >
>>> > > > On Sat, 29 Jan 2022, 10:18 Peat, Tom (Manufacturing, Clayton) <
>>> > > > tom.p...@csiro.au> wrote:
>>> > > >
>>> > > >> Hello Misba,
>>> > > >>
>>> > > >> Doesn't quite look like a phosphate, maybe O-sulfation?
>>> > > >> Maybe just as important as the buffer and crystallisation conditions
>>> > > >> would be how it was expressed? Insect cells?
>>> > > >>
>>> > > >> Best of luck, tom
>>> > > >>
>>> > > >> Tom Peat, PhD
>>> > > >>
>>> > > >> Biomedical Program, CSIRO
>>> > > >> tom.p...@csiro.au
>>> > > >>

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[ccp4mail]

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Re: [ccp4bb] Help with interpreting Tyrosine modification

[Misba Ahmad]

Thank you for your suggestions.
As this is a high resolution structure (1.1Å) I have been refining it with
anisotropic B-factors.
Placing a propionate or modelling a phosphate at this position blows up
during the refinement.
I will inform you if I am successful in figuring this out.

Best
Misbha


On Sat, Jan 29, 2022 at 7:01 PM SHEPARD William <
william.shep...@synchrotron-soleil.fr> wrote:

> Dear Misba,
>
> Perhaps it's a silly question, but have you tried to model in propionate?
> The carboxylate group could make H-bonds to both the Arginine sidechain and
> the the tyrosine OH group. Propionate should show no anomalous signal.
>
> Just my 2-bits worth.
>
> Cheers,
> Bill
>
>
> - Original Message -
> From: "Gerard Bricogne" 
> To: CCP4BB@JISCMAIL.AC.UK
> Sent: Saturday, 29 January, 2022 18:34:26
> Subject: Re: [ccp4bb] Help with interpreting Tyrosine modification
>
> Dear Misba,
>
>  Thank you for your reply and for the very clear picture. I hope you
> will be able to share the result once the mystery is solved.
>
>  With best wishes,
>
>   Gerard.
>
> --
> On Sat, Jan 29, 2022 at 03:32:30PM +0100, Misba Ahmad wrote:
> > Dear Gerard,
> > The data were collected at 0.966Å and I can see the anomalous peaks for
> As
> > at Cysteines which are modified and I have correctly modelled those (see
> > image below). However, at this Tyr, I don't see an anomalous signal.
> >
> > [image: 4.png]
> >
> > On Sat, Jan 29, 2022 at 3:06 PM Gerard Bricogne 
> > wrote:
> >
> > > Dear Misba,
> > >
> > >  A wild guess: have you considered the possibility that this extra
> > > density could be a cacodylate adduct? Cacodylate is well known to react
> > > with
> > > thiols - see
> > >
> > >
> > >
> https://febs.onlinelibrary.wiley.com/doi/pdfdirect/10.1016/0014-5793(72)80224-2
> > >
> > > Here the chemistry is different but you never know. If your data are
> > > redundant enough that you have good anomalous completeness, and were
> > > collected above the As K-edge (11.8667 keV), it might be a good idea to
> > > compute an anomalous difference Fourier and check for the presence of a
> > > peak
> > > at the same location as the highest one in your ordinary difference
> map.
> > >
> > >  Only a wild guess, though ... .
> > >
> > >
> > >  With best wishes,
> > >
> > >   Gerard.
> > >
> > > --
> > > On Sat, Jan 29, 2022 at 12:18:58PM +0100, Misba Ahmad wrote:
> > > > Placing a water molecule satisfies most of the density and forms nice
> > > > H-bonds but there is still some residual density left (8.6 and 5.6
> rmsd).
> > > >
> > > > Best
> > > > Misbha
> > > > [image: 3.png]
> > > >
> > > >
> > > > On Sat, Jan 29, 2022 at 11:05 AM Klaus Futterer <
> k.futte...@bham.ac.uk>
> > > > wrote:
> > > >
> > > > > Looks more like water molecules. Phosphorylation would give a much
> > > bigger
> > > > > peak, and shape of density does not fit either. I don't think this
> is a
> > > > > covalent modification. Model some water molecules and see what the
> > > > > distances are and what difference density is left.
> > > > >
> > > > >
> > > > > Klaus
> > > > >
> > > > >
> > > > > ===
> > > > > Klaus Fütterer, PhD
> > > > > Reader in Structural Biology
> > > > >
> > > > >
> > > > > School of Biosciences
> > > > > LES CollegeEmail:
> > > > > k.futte...@bham.ac.uk
> > > > > University of Birmingham Phone: +44 - 121
> - 414
> > > > > 5895
> > > > > Birmingham, B15 2TT, UK(voice mail messages
> > > > > will forward to my email inbox)
> > > > >
> > > > > My normal working hours are Mon - Fri 8.30 - 5.30 pm.
> > > > >
> > > > >
> > > > > ===
> > > > > --
> > > > > *From:* CCP4 bulletin board  on behalf of
> > > > > misba.ah...@gmail.com 
> > > > > *Sent:* 29 January 2022 09:45:24
> > > > > *To:* CCP4BB@JISCMAIL.AC.UK
> > > > > *Subject:* Re: [ccp4bb] Help with interpreting Tyrosine
> modification
> > > > >
> > > > > Hi Tom,
> > > > > The protein was expressed in E Coli.
> > > > >
> > > > > Best
> > > > > Misbha
> > > > >
> > > > > On Sat, 29 Jan 2022, 10:18 Peat, Tom (Manufacturing, Clayton) <
> > > > > tom.p...@csiro.au> wrote:
> > > > >
> > > > >> Hello Misba,
> > > > >>
> > > > >> Doesn't quite look like a phosphate, maybe O-sulfation?
> > > > >> Maybe just as important as the buffer and crystallisation
> conditions
> > > > >> would be how it was expressed? Insect cells?
> > > > >>
> > > > >> Best of luck, tom
> > > > >>
> > > > >> Tom Peat, PhD
> > > > >>
> > > > >> Biomedical Program, CSIRO
> > > > >> tom.p...@csiro.au
> > > > >>
> > > > >> --
> > > > >> *From:* CCP4 bulletin board  on behalf of
> > > Misba
> > > > >> Ahmad 
> > > > >> *Sent:* Saturday, January 29, 2022 8:12 PM
> > > > >> *To:* CCP4BB@JISCMAIL.AC.UK 
> > > > >> *Subject:* [ccp4bb] Help