[phenixbb] Glycan refinement

Engin Ozkan eozkan at stanford.edu
Tue Nov 10 12:22:21 PST 2009


Hi Blaine,

You are not alone. We recently discovered a few structures deposited 
with incorrect geometries and naming by former lab members. It was 
embarrassing, so we are all paying extra attention now. Getting as much 
help as possible from refinement and validation software is the smart 
thing to do.

Engin

On 11/10/09 11:59 AM, Mooers, Blaine H.M. (HSC) wrote:
> Hi Engin,
>
> I had already gotten as far as the using BMA and MAN.  I will
> give the stereochemistry of my glycans another
> close examination after  reading the papers
> that you referred to.  I think novice  refiners
> of glycoprotein structures like myself
> grossly underestimate the care required to
> refine glycan structures correctly.
>
> Thank you for pointing out the linkage types.
> I will give those a try since restraints beyond
> a simple distance restraint should improve my
> model.
>
> Thank you for your suggestions!
>
> Best regards,
>
> Blaine
>
> **********************************************************
> Blaine Mooers, Ph.D.
> Assistant Professor
> Department of Biochemistry and Molecular Biology
> University of Oklahoma Health Sciences Center
>
> Letter address:                    Shipping address:
> P.O. Box 26901, BRC 466      975 NE 10th Street, BRC 466
> Oklahoma City, OK 73190     Oklahoma City, OK 73104-5419
>
> office: (405) 271-8300   lab: (405) 271-8313  fax:  (405) 271-3910
> email:  blaine-mooers at ouhsc.edu
> http://www.oumedicine.com/body.cfm?id=3877&oTopID=3877
>
> ________________________________________
> From: phenixbb-bounces at phenix-online.org [phenixbb-bounces at phenix-online.org] On Behalf Of Engin Ozkan [eozkan at stanford.edu]
> Sent: Tuesday, November 10, 2009 1:36 PM
> To: PHENIX user mailing list
> Subject: Re: [phenixbb] Glycan refinement
>
> Hi Blaine,
>
> That might not work correctly. You may get the stereochemistry of the
> linkage incorrect if you use just a bond distance restraint.
> You should use linkage types like BETA1-4, or ALPHA1-6, depending on the
> type of the linkage.
> And as I have mentioned in the email before, you should also call your
> beta mannose BMA, and alpha mannose MAN (see the references I mentioned
> in that email).
>
> So something like this would be my guess:
>
>     apply_cif_link {
>       data_link = BETA1-4
>       residue_selection_1 = chain A and resname NAG and resid 902
>       residue_selection_2 = chain A and resname BMA and resid 903
>     }
>     apply_cif_link {
>       data_link = ALPHA1-6
>       residue_selection_1 = chain A and resname BMA and resid 903
>       residue_selection_2 = chain A and resname MAN and resid 904
>     }
>
> Please correct me if I am wrong.
>
> Engin
>
> On 11/10/09 11:23 AM, Mooers, Blaine H.M. (HSC) wrote:
>    
>> Hi Tongqing,
>>
>> Make a sugars.edits ascii file with links like the following between two manoses
>>
>>
>> refinement.geometry_restraints.edits {
>>     bond {
>>       action = *add
>>       atom_selection_1 = name  O2  and chain A and resname MAN and resseq 1490
>>       atom_selection_2 = name  C1  and chain A and resname MAN and resseq 1491
>>       distance_ideal = 1.439000
>>       sigma = 0.020
>>     }
>> }
>>
>> and then include this file when running phenix.refine in the command mode, e.g.
>>
>> phenix.refine --overwrite 715_scala1.mtz 25sugars.pdb 25sugars.edits \
>> refinement.input.xray_data.labels=IMEAN_XDSdataset,SIGIMEAN_XDSdataset \
>> strategy=individual_sites+individual_adp simulated_annealing=true \
>> main.number_of_macro_cycles=10
>>
>> Best regards,
>>
>> Blaine
>>
>>
>>
>>
>> **********************************************************
>> Blaine Mooers, Ph.D.
>> Assistant Professor
>> Department of Biochemistry and Molecular Biology
>> University of Oklahoma Health Sciences Center
>>
>> Letter address:                    Shipping address:
>> P.O. Box 26901, BRC 466      975 NE 10th Street, BRC 466
>> Oklahoma City, OK 73190     Oklahoma City, OK 73104-5419
>>
>> office: (405) 271-8300   lab: (405) 271-8313  fax:  (405) 271-3910
>> email:  blaine-mooers at ouhsc.edu
>> http://www.oumedicine.com/body.cfm?id=3877&oTopID=3877
>>
>> ________________________________________
>> From: phenixbb-bounces at phenix-online.org [phenixbb-bounces at phenix-online.org] On Behalf Of Zhou, Tongqing (NIH/VRC) [E] [tzhou at mail.nih.gov]
>> Sent: Tuesday, November 10, 2009 12:12 PM
>> To: 'phenixbb at phenix-online.org'
>> Subject: [phenixbb] Glycan refinement
>>
>> Dear All,
>>
>> I am refining a structure with a N-linked glycosylation site. There is density that goes beyond the first NAG, at least to MAN3. I know in Phenix there is  data_link = NAG-ASN for the ASN-NAG connection, but I don’t know how to do the “apply_cif_link’ for the extensions such NAG-NAG, NAG-MAN, MAN-MAN…., any suggestions are appreciated.
>>
>> Thanks,
>>
>>
>> Tongqing
>>
>>
>> Tongqing Zhou, Ph.D.
>> Staff Scientist
>> Structural Biology Section
>> Vaccine Research Center, NIAID/NIH
>> Building 40, Room 4607B
>> 40 Convent Drive, MSC3027
>> Bethesda, MD 20892
>> (301) 594-8710 (Tel)
>> (301) 793-0794 (Cell)
>> (301) 480-2658 (Fax)
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>>
>>
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>>
>>      
>
> --
> Engin Özkan
> Post-doctoral Scholar
> Howard Hughes Medical Institute
> Dept of Molecular and Cellular Physiology
> 279 Campus Drive, Beckman Center B173
> Stanford School of Medicine
> Stanford, CA 94305
> ph: (650)-498-7111
>
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>    


-- 
Engin Özkan
Post-doctoral Scholar
Howard Hughes Medical Institute
Dept of Molecular and Cellular Physiology
279 Campus Drive, Beckman Center B173
Stanford School of Medicine
Stanford, CA 94305
ph: (650)-498-7111




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