[phenixbb] Glycan refinement

Tue Nov 10 11:59:32 PST 2009

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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--
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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