[ccp4bb] REFMAC converts alpha-L-fucose into beta-L-fucose

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Fw: conversion of .fcf to 2fo-fc.map and fo-fc.map of ccp4 format
From: U Sam us_x {- at -} HOTMAIL {- dot -} COM
Date: 2007-06-13

Next message:
Subject: Re: ISSUE RESOLVED - REFMAC converts alpha-L-fucose into beta-L-fucose]
From: verdino {- at -} SCRIPPS {- dot -} EDU verdino {- at -} SCRIPPS {- dot -} EDU
Date: 2007-06-13

Subject: REFMAC converts alpha-L-fucose into beta-L-fucose
From: verdino {- at -} SCRIPPS {- dot -} EDU verdino {- at -} SCRIPPS {- dot -} EDU
Date: 2007-06-13

Dear CCP4bb

thanks so much for the helpful information regarding carbohydrate
refinement. Kim's recommendation (see below) for the validation server
worked really well and helped me to finally figure out what is going on.
Seems as if REFMAC5 (part of ccp4-6.0.2 version) is not handling
alpha-L-fucose links correctly - even when I use a correct alpha-linked
model (from the server), and define the link and the sugar appropriately
(see below), it comes back from the refinement with a beta-linkage.

LINK C1 NAG A 501 ND2 ASN A 105
NAG-ASN
LINK O6 NAG A 501 C1 FUC A 506
ALPHA1-6
MODRES NAG A 501 NAG-b-D
RENAME
MODRES FUC A 506 FUC-a-L
RENAME

Maybe someone of the hardcore REFMAC refinement guys (who is familiar with
the libraries) would be willing to check if there is an issue with the
dictionary for alpha-L-fucose or if I am still missing something?????

Thanks for your help, cheers, Petra

> you can use
> http://www.glycosciences.de/modeling/sweet2/doc/index.php
> to get a pdb file of your sugar
>
> and after fitting in density and refinement use
> http://www.dkfz-heidelberg.de/spec/glycosciences.de/tools/pdbcare/
> to check the stereochemistry
>
> this should identify if there is a refmac dictionary problem
>
> your sugar is a "Core Fucosylated And Bisected N-glycan (N-Link 2)"
> [see the sweet doc pages]
>
> you can make the IUPAC notation in plain ASCII
>
> a-D-Manp-(1-6)+
>

>
a-L-Fucp-(1-6)+
>

>
b-D-GlcpNAc-(1-4)-Asn
>

> b-D-Manp-(1-4)-b-D-GlcpNAc-(1-4)+
>

>

>

>

>

> a-D-Manp-(1-3)+
>
> and drop this into sweet and get an idealised torsion angle(d) pdb
>
>
> an o/p is www.ebi.ac.uk/~henrick/sug.pdb
>
> unfortunately the original pdb output is not exactly pdb
> you have to move the residue name column and the
> ASN is labelled as UNK
>
> the torsion angles are from the database
> http://www.glycosciences.de/modeling/glycomapsdb/
>
> if you want to check your fitted conformation with what is expected
> (a lot more freedom than a ramachandran but basically
> the same type of plots)
>
>
>
>
>
> --
> Kim HENRICK henrick@ebi.ac.uk ::telephone: +44 (0) 1223 494629
>

--
Petra Verdino, PhD
Research Associate
The Scripps Research Institute, BCC206
10550 North Torrey Pines Road
CA 92037 La Jolla, USA
tel:1-858-784-2294
fax:1-858-784-2980

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Fw: conversion of .fcf to 2fo-fc.map and fo-fc.map of ccp4 format
From: U Sam us_x {- at -} HOTMAIL {- dot -} COM
Date: 2007-06-13