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(-) Description

Title :  CRYSTAL STRUCTURE OF PUTATIVE SUGAR BINDING PROTEIN (YP_001299726.1) FROM BACTEROIDES VULGATUS ATCC 8482 AT 1.90 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  26 Oct 09  (Deposition) - 10 Nov 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Putative Sugar Binding Protein, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Putative Sugar Binding Protein (Yp_001299726. 1) From Bacteroides Vulgatus Atcc 8482 At 1. 9 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE SUGAR BINDING PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: SEQUENCE DATABASE RESIDUES 23-482
    Gene: BVU_2446
    Organism Scientific: BACTEROIDES VULGATUS ATCC 8482
    Organism Taxid: 435590
    Strain: ATCC 8482 / DSM 1447 / NCTC 11154
    Synonym: PUTATIVE OUTER MEMBRANE PROTEIN, PROBABLY INVOLVED IN NUTRIENT BINDING

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 45)

Asymmetric Unit (4, 45)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2EDO15Ligand/Ion1,2-ETHANEDIOL
3MSE26Mod. Amino AcidSELENOMETHIONINE
4PO42Ligand/IonPHOSPHATE ION
Biological Unit 1 (3, 19)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2EDO5Ligand/Ion1,2-ETHANEDIOL
3MSE13Mod. Amino AcidSELENOMETHIONINE
4PO41Ligand/IonPHOSPHATE ION
Biological Unit 2 (3, 24)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2EDO10Ligand/Ion1,2-ETHANEDIOL
3MSE13Mod. Amino AcidSELENOMETHIONINE
4PO41Ligand/IonPHOSPHATE ION

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:282 , GLN A:343 , GLU A:346 , ASP A:350 , ASN A:352 , HOH A:529BINDING SITE FOR RESIDUE CA A 501
02AC2SOFTWAREASN A:455 , PHE A:456 , HIS A:457 , LYS B:398BINDING SITE FOR RESIDUE PO4 A 1
03AC3SOFTWAREGLY A:156 , TYR A:157 , SER A:166 , LEU A:167 , LEU A:460 , ASN A:477 , PRO A:478 , HOH A:506BINDING SITE FOR RESIDUE EDO A 4
04AC4SOFTWAREASN A:375 , GLU A:396 , GLY A:397 , HOH A:538 , HOH A:902 , EDO B:3 , GLN B:344BINDING SITE FOR RESIDUE EDO A 5
05AC5SOFTWAREARG A:64 , HOH A:519 , HOH A:714 , HOH A:741 , HOH A:829 , HOH A:882BINDING SITE FOR RESIDUE EDO A 8
06AC6SOFTWARETYR A:107 , GLU A:467 , HOH A:792 , HOH A:808 , HOH A:815BINDING SITE FOR RESIDUE EDO A 14
07AC7SOFTWAREASP A:453 , ASN A:455 , ASN B:404 , HOH B:528BINDING SITE FOR RESIDUE EDO A 15
08AC8SOFTWAREASN B:282 , GLN B:343 , GLU B:346 , ASP B:350 , ASN B:352 , HOH B:520BINDING SITE FOR RESIDUE CA B 501
09AC9SOFTWARELYS A:398 , EDO B:16 , ASN B:455 , PHE B:456 , HIS B:457 , HOH B:552BINDING SITE FOR RESIDUE PO4 B 2
10BC1SOFTWAREEDO A:5 , GLN B:343 , GLN B:344 , GLY B:345 , GLU B:346BINDING SITE FOR RESIDUE EDO B 3
11BC2SOFTWAREHOH A:780 , GLU B:403 , LEU B:406 , ASP B:407 , ARG B:419BINDING SITE FOR RESIDUE EDO B 6
12BC3SOFTWARETRP B:103 , PRO B:182 , GLU B:467 , HOH B:484 , HOH B:970BINDING SITE FOR RESIDUE EDO B 7
13BC4SOFTWAREASN A:404 , EDO B:16 , ASP B:453 , ASN B:455BINDING SITE FOR RESIDUE EDO B 9
14BC5SOFTWARETYR B:299 , PHE B:329 , ASP B:330 , LYS B:331BINDING SITE FOR RESIDUE EDO B 10
15BC6SOFTWAREGLY B:156 , TYR B:157 , SER B:166 , LEU B:167 , LEU B:460 , ASN B:477 , PRO B:478 , HOH B:733 , HOH B:778BINDING SITE FOR RESIDUE EDO B 11
16BC7SOFTWARELYS B:325 , ILE B:326 , LEU B:327 , SER B:328 , ASN B:338 , HOH B:830BINDING SITE FOR RESIDUE EDO B 12
17BC8SOFTWARETYR B:61 , ASP B:150 , ARG B:153 , ARG B:225 , LEU B:355 , HOH B:582 , HOH B:869BINDING SITE FOR RESIDUE EDO B 13
18BC9SOFTWARELYS A:398 , PO4 B:2 , EDO B:9 , EDO B:17 , TYR B:452 , ASP B:453 , ASN B:455 , PHE B:456BINDING SITE FOR RESIDUE EDO B 16
19CC1SOFTWAREEDO B:16 , TYR B:449 , GLU B:451 , HOH B:552BINDING SITE FOR RESIDUE EDO B 17

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3KEZ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3KEZ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3KEZ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3KEZ)

(-) Exons   (0, 0)

(no "Exon" information available for 3KEZ)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:447
 aligned with A6L340_BACV8 | A6L340 from UniProtKB/TrEMBL  Length:482

    Alignment length:447
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       
         A6L340_BACV8    35 ETSINVLSDIEFTLNGIYSTMQSSDAYSGRLVYYGDVTGDDMQAVSSTKRTGNYYRFNFTKDNGPSSHWSYLYSIIQNCNLILMNVDKLSIDEDETEYKNDLKGQALAIRGMALFDLTRIFGYPYLKDNGASLGVPIVKELSTIDSKPARNTVAECYTEIISDLKNSTELLSGDFNKGKVNRWAAMTLLSRVYLYKGEYNEALTMAENAIKGAEKEGYALWTNEEYPTAWGNDASASNPGEILFEIVNLTTDSPGKESMGYLNSYNGYDDMCITCSFYQLLKKDPKDVRLKILSFDKKYYAYVNKYQPQQGENITDANIPLIRLSEAYLNAAEAAVQTGDNAKAVKYLNSIVQRANPENSVEGKTLTLENVLDERRKELVAEGHRMYDVIRNGMTVKRIDVKDSDINKTKHNTAYMEYDWNFHKILLPIPKKEMDANPNMKQNPGYV 481
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhh......hhhhhhhhhh...eee......hhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.......................hhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhh...........eeeee...........hhhhhh.......eeehhhhhhhhhh...hhhhh.eeee...eeee.........hhhhh.eeeeehhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhh...hhhhhhhh....ee.....hhhhh.........ee...hhhhh...hhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kez A  35 ETSINVLSDIEFTLNGIYSTmQSSDAYSGRLVYYGDVTGDDmQAVSSTKRTGNYYRFNFTKDNGPSSHWSYLYSIIQNCNLILmNVDKLSIDEDETEYKNDLKGQALAIRGmALFDLTRIFGYPYLKDNGASLGVPIVKELSTIDSKPARNTVAECYTEIISDLKNSTELLSGDFNKGKVNRWAAmTLLSRVYLYKGEYNEALTmAENAIKGAEKEGYALWTNEEYPTAWGNDASASNPGEILFEIVNLTTDSPGKESmGYLNSYNGYDDmCITCSFYQLLKKDPKDVRLKILSFDKKYYAYVNKYQPQQGENITDANIPLIRLSEAYLNAAEAAVQTGDNAKAVKYLNSIVQRANPENSVEGKTLTLENVLDERRKELVAEGHRmYDVIRNGmTVKRIDVKDSDINKTKHNTAYmEYDWNFHKILLPIPKKEmDANPNmKQNPGYV 481
                                    44        54|       64        74 |      84        94       104       114   |   124       134       144 |     154       164       174       184       194       204       214     | 224       234    |  244       254       264       274       284       294       304|      314       324       334       344       354       364       374       384       394       404       414     | 424   |   434       444     | 454       464   |   474       
                                               55-MSE               76-MSE                                   118-MSE                     146-MSE                                                                   220-MSE            239-MSE                                               293-MSE     305-MSE                                                                                                            420-MSE 428-MSE               450-MSE           468-MSE |       
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 474-MSE   


Chain B from PDB  Type:PROTEIN  Length:448
 aligned with A6L340_BACV8 | A6L340 from UniProtKB/TrEMBL  Length:482

    Alignment length:448
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474        
         A6L340_BACV8    35 ETSINVLSDIEFTLNGIYSTMQSSDAYSGRLVYYGDVTGDDMQAVSSTKRTGNYYRFNFTKDNGPSSHWSYLYSIIQNCNLILMNVDKLSIDEDETEYKNDLKGQALAIRGMALFDLTRIFGYPYLKDNGASLGVPIVKELSTIDSKPARNTVAECYTEIISDLKNSTELLSGDFNKGKVNRWAAMTLLSRVYLYKGEYNEALTMAENAIKGAEKEGYALWTNEEYPTAWGNDASASNPGEILFEIVNLTTDSPGKESMGYLNSYNGYDDMCITCSFYQLLKKDPKDVRLKILSFDKKYYAYVNKYQPQQGENITDANIPLIRLSEAYLNAAEAAVQTGDNAKAVKYLNSIVQRANPENSVEGKTLTLENVLDERRKELVAEGHRMYDVIRNGMTVKRIDVKDSDINKTKHNTAYMEYDWNFHKILLPIPKKEMDANPNMKQNPGYVD 482
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) SusD-like_3-3kezB03 B:35-228                                                                                                                                                                      ---------------------------------------------SusD-3kezB01 B:274-480                                                                                                                                                                                         -- Pfam domains (1)
           Pfam domains (2) SusD-like_3-3kezB04 B:35-228                                                                                                                                                                      ---------------------------------------------SusD-3kezB02 B:274-480                                                                                                                                                                                         -- Pfam domains (2)
         Sec.struct. author .....hhhhhhhhhhhhhhhhh......hhhhhhhhhh...eee......hhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.......................hhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.......hhhhhh...........eeeee...........hhhhhh.......eeehhhhhhhhhh...hhhhh.eeee...eeee.........hhhhh.eeeeehhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhh....hhhhhhhhh...ee.....hhhhh.........ee...hhhhh...hhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kez B  35 ETSINVLSDIEFTLNGIYSTmQSSDAYSGRLVYYGDVTGDDmQAVSSTKRTGNYYRFNFTKDNGPSSHWSYLYSIIQNCNLILmNVDKLSIDEDETEYKNDLKGQALAIRGmALFDLTRIFGYPYLKDNGASLGVPIVKELSTIDSKPARNTVAECYTEIISDLKNSTELLSGDFNKGKVNRWAAmTLLSRVYLYKGEYNEALTmAENAIKGAEKEGYALWTNEEYPTAWGNDASASNPGEILFEIVNLTTDSPGKESmGYLNSYNGYDDmCITCSFYQLLKKDPKDVRLKILSFDKKYYAYVNKYQPQQGENITDANIPLIRLSEAYLNAAEAAVQTGDNAKAVKYLNSIVQRANPENSVEGKTLTLENVLDERRKELVAEGHRmYDVIRNGmTVKRIDVKDSDINKTKHNTAYmEYDWNFHKILLPIPKKEmDANPNmKQNPGYVD 482
                                    44        54|       64        74 |      84        94       104       114   |   124       134       144 |     154       164       174       184       194       204       214     | 224       234    |  244       254       264       274       284       294       304|      314       324       334       344       354       364       374       384       394       404       414     | 424   |   434       444     | 454       464   |   474        
                                               55-MSE               76-MSE                                   118-MSE                     146-MSE                                                                   220-MSE            239-MSE                                               293-MSE     305-MSE                                                                                                            420-MSE 428-MSE               450-MSE           468-MSE |        
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 474-MSE
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3KEZ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3KEZ)

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: TPR (230)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (A6L340_BACV8 | A6L340)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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