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CCP4BB  April 2013

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Subject:

Alternate sugar conformations in refmac 5.5.0110

From:

Markus Meier <[log in to unmask]>

Reply-To:

[log in to unmask]

Date:

Thu, 18 Apr 2013 15:16:49 -0500

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (79 lines)

Dear all,

I am trying to refine a beta-D-N-Acetyl glucosamine moiety (NAG) linked
to an asparagine (ASN) in Refmac.
(version CCP4 6.3: Refmac_5.5.0110     version 5.5.0110 : 08/05/10)

The sugar has two alternate conformations that occupy the same position in the electron
density but are rotated 180° relative to each other. Even though I have
defined two alternate conformations for the asparagine side chain, the
sugar and the beta-link, Refmac pushes the two conformations apart, out of the electron
density (while still honouring the link to Asn). So it seems that Refmac applies repulsive
forces between the alternate conformations.

Did anyone else experience this and/or can suggest a fix?
All help is very much appreciated!

My definitions for the alternate conformations in the PDB file are below:

LINKR        C1 ANAG E   1                 ND2AASN A 116                NAG-ASN
LINKR        C1 BNAG E   1                 ND2BASN A 116                NAG-ASN
HETATM  125  C1 ANAG E   1      30.978  40.626 -25.446  0.50 98.96      E    C
HETATM  126  C2 ANAG E   1      30.428  41.897 -26.138  0.50100.81      E    C
HETATM  127  N2 ANAG E   1      29.783  41.751 -27.447  0.50 94.26      E    N
HETATM  128  C7 ANAG E   1      28.807  42.561 -27.924  0.50 89.45      E    C
HETATM  129  O7 ANAG E   1      28.325  42.377 -29.035  0.50 83.16      E    O
HETATM  130  C8 ANAG E   1      28.252  43.720 -27.128  0.50 87.63      E    C
HETATM  131  C3 ANAG E   1      31.618  42.847 -26.221  0.50102.77      E    C
HETATM  132  O3 ANAG E   1      31.420  43.888 -27.159  0.50102.25      E    O
HETATM  133  C4 ANAG E   1      31.840  43.369 -24.802  0.50103.37      E    C
HETATM  134  O4 ANAG E   1      32.969  44.217 -24.782  0.50104.91      E    O
HETATM  135  C5 ANAG E   1      32.040  42.223 -23.785  0.50 94.99      E    C
HETATM  136  C6 ANAG E   1      31.564  42.633 -22.381  0.50 86.60      E    C
HETATM  137  O6 ANAG E   1      32.632  42.591 -21.462  0.50 77.76      E    O
HETATM  138  O5 ANAG E   1      31.458  40.954 -24.130  0.50 99.19      E    O
HETATM  139  C1 BNAG E   1      30.271  40.925 -24.108  0.50 98.96      E    C
HETATM  140  C2 BNAG E   1      31.415  41.878 -23.684  0.50100.81      E    C
HETATM  141  N2 BNAG E   1      32.048  41.664 -22.378  0.50 94.26      E    N
HETATM  142  C7 BNAG E   1      33.331  41.981 -22.079  0.50 89.45      E    C
HETATM  143  O7 BNAG E   1      33.784  41.778 -20.959  0.50 83.16      E    O
HETATM  144  C8 BNAG E   1      34.276  42.586 -23.092  0.50 87.63      E    C
HETATM  145  C3 BNAG E   1      30.816  43.277 -23.775  0.50102.77      E    C
HETATM  146  O3 BNAG E   1      31.569  44.240 -23.061  0.50102.25      E    O
HETATM  147  C4 BNAG E   1      30.718  43.597 -25.266  0.50103.37      E    C
HETATM  148  O4 BNAG E   1      30.115  44.862 -25.440  0.50104.91      E    O
HETATM  149  C5 BNAG E   1      29.907  42.532 -26.038  0.50 94.99      E    C
HETATM  150  C6 BNAG E   1      30.373  42.426 -27.500  0.50 86.60      E    C
HETATM  151  O6 BNAG E   1      29.320  42.743 -28.381  0.50 77.76      E    O
HETATM  152  O5 BNAG E   1      29.866  41.216 -25.458  0.50 99.19      E    O
ATOM    745  N   ASN A 116      27.207  36.475 -25.453  1.00 62.15      A    N
ATOM    746  CA AASN A 116      28.475  37.144 -25.135  0.50 61.77      A    C
ATOM    747  CB AASN A 116      28.182  38.336 -24.223  0.50 69.02      A    C
ATOM    748  CG AASN A 116      29.037  39.555 -24.495  0.50 79.45      A    C
ATOM    749  OD1AASN A 116      28.656  40.644 -24.047  0.50 83.18      A    O
ATOM    750  ND2AASN A 116      30.178  39.419 -25.218  0.50 87.72      A    N
ATOM    751  C   ASN A 116      29.353  36.143 -24.389  1.00 53.28      A    C
ATOM    752  O   ASN A 116      29.778  36.380 -23.266  1.00 48.83      A    O
ATOM    753  CA BASN A 116      28.575  37.144 -25.135  0.50 61.77      A    C
ATOM    754  CB BASN A 116      28.282  38.336 -24.223  0.50 69.02      A    C
ATOM    755  CG BASN A 116      29.487  39.201 -23.920  0.50 79.45      A    C
ATOM    756  OD1BASN A 116      30.611  38.710 -24.084  0.50 83.18      A    O
ATOM    757  ND2BASN A 116      29.299  40.471 -23.478  0.50 87.72      A    N

The Refmac log output shows that link description was recognized correctly for each conformation:
  WARNING : residue: NAG                 1  chain:EE
            atom: "O1  " is absent in coord_file
  WARNING : link(spec):NAG-ASN  is found dist =     1.466 ideal_dist=     1.439
            ch:EE   res:   1  NAG              at:C1  A->AA   res: 116  ASN              at:ND2 A
  WARNING : link(spec):NAG-ASN  is found dist =     1.244 ideal_dist=     1.439
            ch:EE   res:   1  NAG              at:C1  B->AA   res: 116  ASN              at:ND2 B


Best regards,
Markus

-- 
Markus Meier, Ph.D.
University of Manitoba
Department of Chemistry
144 Dysart Road

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