Re: [ccp4bb] Automatic LINK generation
Dear Hailiang There are several protein-sugar and sugar-sugar link defined in the standard refmac library. You may try running refmac with the default options with the input pdb file in which - sugar residues included, - no LINK record are specified. If all required links are in the refmac's library, the refinement will work, and the output PDB will contain the LINK records, e.g. ... LINKC1 NAG A1539ND2 ASN A 341NAG-ASN LINK NAG A1539 NAG A1540BETA1-4 MODRES NAG A 1539 NAG-b-D RENAME MODRES NAG A 1540 NAG-b-D RENAME ... In the log file you will see: ... WARNING : link: NAG--NAG is without link_id link will be created with covalent bond only. Bond= 1.430 ... WARNING : link:NAG-ASN is found dist = 1.427 ideal_dist= 1.439 ch:AA res: 341 ASN at:ND2 .-Aj res:1539 NAG at:C1 . WARNING : link:BETA1-4 is found dist = 1.430 ideal_dist= 1.439 ch:Aj res:1539 NAG at:O4 .-Ak res:1540 NAG at:C1 . ... The last two warnings actually mean that everything is fine. Ignore the first warning, as it is overridden by the third one. All the best Andrey
Re: [ccp4bb] Automatic LINK generation
Dear Hailiang, While apparently no response came, here my 2 cents: Even if there would be an automatic utitility to generate links based on distances, I would never use it. Either the sugars have been properly refined and then the link cards are present in the pdb file, or the sugars have been fitted manually and may have been real space refined in coot or some other model-building program. In this case, the sugar positions are likely off, since sugars are very often rather disordered and have poor electron density. In this case distance-based link generators very likely will make wrong connections. I just cut and paste link cards from an other pdb file and manually edit them. I eagerly await the moment there will be a create link option in coot, where you just click on the two atoms to be linked and the link card gets generated. Best, Herman -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Hailiang Zhang Sent: Wednesday, March 09, 2011 1:01 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Automatic LINK generation Hi there, I am trying to build the LINK information in PDB header for sugar-containing protein, and I am wondering whether there is some utility in CCP4 (or any others) can do it automatically (eg by measuring inter-sugar distances). Thanks in advance! Best Regards, Hailiang
Re: [ccp4bb] Automatic LINK generation
Dear Hailiang, as Herman Schreuder already wrote sugars are quite likely to contain errors. We are developing the PDB CArbohydrate REsidue check tool (pdb-care) in our group to help crystallographers locating problems in sugars. There will be an update soon, which includes checks for potentially missing LINK records and indicates the atoms that should be linked (and also checks, if linkages result in proper residues, i.e. if there are residues linked to a protein that are not known to occur in glycoproteins, such as NDG (a-D-GlcpNAc) in N-glycan chains). A beta version of the upcoming update is now available at http://www.glycosciences.de/tools/pdbcare2/ - it might help you to identify the atoms that are to be linked and to find potential issues before publishing the structure. Best regards, Thomas
Re: [ccp4bb] Automatic LINK generation
Does anybody know the pdb codes with proteins with O-linked sugars on THR. I support a program to help interpret sugars in poor electron density by stabilizing links. Coot helps a bit but branching poses a problem. Rather than based on distance like coot operates at present it should be best if one could specify the type of link. I have crystals where sugars are in poor electron density. I can recognize sialic acid moieties at a crystal contact with symmetry related molecule, but fitting the weak density for the sugars leading to the crystal contact is almost impossible. There are good reasons to combine knowledge of normal human glycosylation with weak electron density to produce a reasonable model. With natural products and heterogeneous sugars, the density in never going to be fantastic except for the few sugar moieties close to the protein. Yet interpreting all existing density may be a step better than outright modeling. Enrico. On Thu, 10 Mar 2011 09:45:57 +0100, herman.schreu...@sanofi-aventis.com wrote: Dear Hailiang, While apparently no response came, here my 2 cents: Even if there would be an automatic utitility to generate links based on distances, I would never use it. Either the sugars have been properly refined and then the link cards are present in the pdb file, or the sugars have been fitted manually and may have been real space refined in coot or some other model-building program. In this case, the sugar positions are likely off, since sugars are very often rather disordered and have poor electron density. In this case distance-based link generators very likely will make wrong connections. I just cut and paste link cards from an other pdb file and manually edit them. I eagerly await the moment there will be a create link option in coot, where you just click on the two atoms to be linked and the link card gets generated. Best, Herman -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Hailiang Zhang Sent: Wednesday, March 09, 2011 1:01 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Automatic LINK generation Hi there, I am trying to build the LINK information in PDB header for sugar-containing protein, and I am wondering whether there is some utility in CCP4 (or any others) can do it automatically (eg by measuring inter-sugar distances). Thanks in advance! Best Regards, Hailiang -- Enrico A. Stura D.Phil. (Oxon) ,Tel: 33 (0)1 69 08 4302 Office Room 19, Bat.152, Tel: 33 (0)1 69 08 9449Lab LTMB, SIMOPRO, IBiTec-S, CE Saclay, 91191 Gif-sur-Yvette, FRANCE http://www-dsv.cea.fr/en/institutes/institute-of-biology-and-technology-saclay-ibitec-s/unites-de-recherche/department-of-molecular-engineering-of-proteins-simopro/molecular-toxinology-and-biotechnology-laboratory-ltmb/crystallogenesis-e.-stura http://www.chem.gla.ac.uk/protein/mirror/stura/index2.html e-mail: est...@cea.fr Fax: 33 (0)1 69 08 90 71
Re: [ccp4bb] Automatic LINK generation
Dear Enrico, you can find information on PDB entries with carbohydrates in the GLYCOSCIENCES.de database: http://www.glycosciences.de/database/index.php To find entries with O-Glycans linked to Thr you can use the substructure search at http://www.glycosciences.de/database/start.php?action=form_structure_matrix (please make sure that you tick the checkbox with PDB entries to limit the search to carbohydrates that are found in the PDB). Just type THR into the center field of one of the upper input area. This will reveal all glycan chains in the database that feature a Thr residue and are represented in PDB structures. There might be more entries in the PDB than in our database, because we try and skip erroneous structures, e.g. those with a mismatch between PDB residue name and residue present in the coordinates (unless it is obvious that the coordinates are correct and just the residue name is wrong, but for O-glycans that's often difficult to tell). Best regards, Thomas
