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(-) Description

Title :  CRYSTAL STRUCTURE OF A SUSD SUPERFAMILY PROTEIN (BVU_0732) FROM BACTEROIDES VULGATUS ATCC 8482 AT 1.80 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  11 May 10  (Deposition) - 02 Jun 10  (Release) - 02 Jun 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Ragb, Susd And Hypothetical Proteins, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Polysaccharide Binding Protein, Saccharide Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of A Susd Superfamily Protein (Bvu_0732) From Bacteroides Vulgatus Atcc 8482 At 1. 80 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - SUSD SUPERFAMILY 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
    Gene: BVU_0732
    Organism Scientific: BACTEROIDES VULGATUS
    Organism Taxid: 435590
    Strain: ATCC 8482 / DSM 1447 / NCTC 11154
    Synonym: PUTATIVE OUTER MEMBRANE PROTEIN

 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, 42)

Asymmetric Unit (4, 42)
No.NameCountTypeFull Name
1EDO18Ligand/Ion1,2-ETHANEDIOL
2MSE22Mod. Amino AcidSELENOMETHIONINE
3NA1Ligand/IonSODIUM ION
4PO41Ligand/IonPHOSPHATE ION
Biological Unit 1 (2, 19)
No.NameCountTypeFull Name
1EDO8Ligand/Ion1,2-ETHANEDIOL
2MSE11Mod. Amino AcidSELENOMETHIONINE
3NA-1Ligand/IonSODIUM ION
4PO4-1Ligand/IonPHOSPHATE ION
Biological Unit 2 (3, 22)
No.NameCountTypeFull Name
1EDO10Ligand/Ion1,2-ETHANEDIOL
2MSE11Mod. Amino AcidSELENOMETHIONINE
3NA-1Ligand/IonSODIUM ION
4PO41Ligand/IonPHOSPHATE ION

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:280 , SER A:281 , ASP A:284 , PRO A:286 , LEU A:351 , HOH A:593BINDING SITE FOR RESIDUE NA A 502
02AC2SOFTWAREGLU A:78 , ALA A:331 , HOH A:581 , HOH A:692 , VAL B:261 , ALA B:262BINDING SITE FOR RESIDUE EDO A 503
03AC3SOFTWAREPHE A:64 , ASN A:354 , ASN A:355 , VAL A:356 , GLY A:419 , GLU A:420 , HOH A:717BINDING SITE FOR RESIDUE EDO A 505
04AC4SOFTWAREPHE A:106 , PRO A:181 , HOH A:669 , HOH A:980 , HOH A:1060 , HOH A:1241 , HOH A:1371BINDING SITE FOR RESIDUE EDO A 506
05AC5SOFTWAREMSE A:401 , ALA A:402 , TYR A:404 , EDO A:520 , HOH A:1526 , LEU B:314BINDING SITE FOR RESIDUE EDO A 507
06AC6SOFTWARETYR A:255 , ALA A:263 , TRP A:264 , VAL A:356 , HOH A:652 , HOH A:906 , HOH A:985BINDING SITE FOR RESIDUE EDO A 509
07AC7SOFTWARETYR A:59 , ARG A:152 , ARG A:224 , VAL A:357 , GLU A:420 , GLY A:421 , HOH A:828 , HOH A:1093BINDING SITE FOR RESIDUE EDO A 516
08AC8SOFTWARELEU A:254 , ARG A:392 , HOH A:562 , HOH A:603BINDING SITE FOR RESIDUE EDO A 519
09AC9SOFTWARECYS A:372 , GLY A:375 , MSE A:401 , TYR A:404 , EDO A:507 , HOH A:1132 , HOH A:1568BINDING SITE FOR RESIDUE EDO A 520
10BC1SOFTWAREARG A:288 , TYR A:293 , HOH A:773 , TYR B:298 , LYS B:347 , HOH B:543 , HOH B:572 , HOH B:602 , HOH B:790 , HOH B:800 , HOH B:1163BINDING SITE FOR RESIDUE PO4 B 501
11BC2SOFTWAREPHE B:64 , ASN B:355 , VAL B:356 , GLY B:419 , GLU B:420 , HOH B:638BINDING SITE FOR RESIDUE EDO B 504
12BC3SOFTWARETYR B:255 , ALA B:263 , TRP B:264 , VAL B:356 , HOH B:662 , HOH B:799 , HOH B:829BINDING SITE FOR RESIDUE EDO B 508
13BC4SOFTWARESER B:100 , TRP B:102 , GLY B:103 , HOH B:1374 , HOH B:1504 , HOH B:1616BINDING SITE FOR RESIDUE EDO B 510
14BC5SOFTWAREGLY A:176 , THR A:177 , HOH A:604 , GLU B:79 , GLY B:299 , TYR B:300 , LYS B:302BINDING SITE FOR RESIDUE EDO B 511
15BC6SOFTWAREASN A:328 , LEU B:314 , PRO B:317 , GLY B:322 , HIS B:323 , HOH B:588 , HOH B:685 , HOH B:813 , HOH B:1221BINDING SITE FOR RESIDUE EDO B 512
16BC7SOFTWARETYR B:59 , ARG B:152 , ARG B:224 , VAL B:357 , GLU B:420 , GLY B:421 , HOH B:1165 , HOH B:1193BINDING SITE FOR RESIDUE EDO B 513
17BC8SOFTWAREASP B:72 , THR B:433 , ILE B:434 , VAL B:435 , HOH B:838 , HOH B:1009BINDING SITE FOR RESIDUE EDO B 514
18BC9SOFTWAREARG B:110 , PRO B:181 , GLN B:464 , HOH B:870BINDING SITE FOR RESIDUE EDO B 515
19CC1SOFTWARELEU B:254 , ARG B:392 , HOH B:570 , HOH B:936BINDING SITE FOR RESIDUE EDO B 517
20CC2SOFTWARELEU A:383 , ASN A:387 , HOH A:735 , HOH A:989 , GLN B:307 , GLU B:311 , HOH B:1032BINDING SITE FOR RESIDUE EDO B 518

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Thr A:285 -Pro A:286

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3MYV)

(-) 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:445
 aligned with A6KYC4_BACV8 | A6KYC4 from UniProtKB/TrEMBL  Length:480

    Alignment length:445
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475     
         A6KYC4_BACV8    36 FRTVTDVDNAVNGLYDLMSGSGYYGAAMFAYGDMKGDDMQSSEESGVCNTCYMFNHRPNSLNAGSLWGRPFYILREAWNILNAIAEGKIESGDEKKLNALKGETMAVIALCQFDLTRCFGYPYTKDKGASLGAPLIDHLVGTYENPPRSTVAQAYDFIIETLEEAVTLMSEEKNNGRMNKYAARALLARIYLYHDDNRKAFDLADQLIKDADTSGSYALYPHEKYVAAWSVEAKFGSESFFEIANSVDDTPGRDSWGYLLNWYGYQKGFVTQKYAEQMLADPGDVRGHLLEENKYAGKTVWWLYKLRGTDLKTAPLECNNVVLRLSEVYLIAAEAGCKLGGDAAVQGLGYLNEIVKRGNPDNEVTMADYTLDRVLDERSKELVGEGHRFFDLLRNGKTIVRKGGYHLPSVDEEVDWDFYKCVLPIPEDQFIFSPEMEQNPGYPKN 480
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhh......hhhhhhhhhh...eee....hhhhhhhh.............hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh....eeee.............eeehhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh....eeeee...........hhhhhh.......eeehhhhhhhhhh...hhhhh.eeeeee..eeeeee................eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh...hhhhhhhhh...ee............ee...hhhhh...hhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3myv A  36 FRTVTDVDNAVNGLYDLmSGSGYYGAAmFAYGDmKGDDmQSSEESGVCNTCYmFNHRPNSLNAGSLWGRPFYILREAWNILNAIAEGKIESGDEKKLNALKGETmAVIALCQFDLTRCFGYPYTKDKGASLGAPLIDHLVGTYENPPRSTVAQAYDFIIETLEEAVTLmSEEKNNGRmNKYAARALLARIYLYHDDNRKAFDLADQLIKDADTSGSYALYPHEKYVAAWSVEAKFGSESFFEIANSVDDTPGRDSWGYLLNWYGYQKGFVTQKYAEQmLADPGDVRGHLLEENKYAGKTVWWLYKLRGTDLKTAPLECNNVVLRLSEVYLIAAEAGCKLGGDAAVQGLGYLNEIVKRGNPDNEVTmADYTLDRVLDERSKELVGEGHRFFDLLRNGKTIVRKGGYHLPSVDEEVDWDFYKCVLPIPEDQFIFSPEmEQNPGYPKN 480
                                    45       |55       |65   |    75        85  |     95       105       115       125       135    |  145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395     | 405       415       425       435       445       455       465     | 475     
                                            53-MSE    63-MSE |    |            88-MSE                                             140-MSE                                                         204-MSE  213-MSE                                                                                             313-MSE                                                                                 401-MSE                                                               471-MSE     
                                                            69-MSE|                                                                                                                                                                                                                                                                                                                                                                                                                      
                                                                 74-MSE                                                                                                                                                                                                                                                                                                                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:444
 aligned with A6KYC4_BACV8 | A6KYC4 from UniProtKB/TrEMBL  Length:480

    Alignment length:444
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475    
         A6KYC4_BACV8    36 FRTVTDVDNAVNGLYDLMSGSGYYGAAMFAYGDMKGDDMQSSEESGVCNTCYMFNHRPNSLNAGSLWGRPFYILREAWNILNAIAEGKIESGDEKKLNALKGETMAVIALCQFDLTRCFGYPYTKDKGASLGAPLIDHLVGTYENPPRSTVAQAYDFIIETLEEAVTLMSEEKNNGRMNKYAARALLARIYLYHDDNRKAFDLADQLIKDADTSGSYALYPHEKYVAAWSVEAKFGSESFFEIANSVDDTPGRDSWGYLLNWYGYQKGFVTQKYAEQMLADPGDVRGHLLEENKYAGKTVWWLYKLRGTDLKTAPLECNNVVLRLSEVYLIAAEAGCKLGGDAAVQGLGYLNEIVKRGNPDNEVTMADYTLDRVLDERSKELVGEGHRFFDLLRNGKTIVRKGGYHLPSVDEEVDWDFYKCVLPIPEDQFIFSPEMEQNPGYPK 479
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------SusD-3myvB01 B:205-477                                                                                                                                                                                                                                                           -- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------SusD-3myvB02 B:205-477                                                                                                                                                                                                                                                           -- Pfam domains (2)
           Pfam domains (3) SusD-like_3-3myvB03 B:36-227                                                                                                                                                                    ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains (3)
           Pfam domains (4) SusD-like_3-3myvB04 B:36-227                                                                                                                                                                    ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains (4)
         Sec.struct. author ..hhhhhhhhhhhhhhhhh......hhhhhhhhhh...eee....hhhhhhhhh............hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh....eeee.............eeehhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhh........eeeee.......hhhhhhhhhhh......eeehhhhhhhhhh...hhhhh.eeeeee..eeeeee................eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh...hhhhhhhh....ee............ee...hhhhh.....hhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3myv B  36 FRTVTDVDNAVNGLYDLmSGSGYYGAAmFAYGDmKGDDmQSSEESGVCNTCYmFNHRPNSLNAGSLWGRPFYILREAWNILNAIAEGKIESGDEKKLNALKGETmAVIALCQFDLTRCFGYPYTKDKGASLGAPLIDHLVGTYENPPRSTVAQAYDFIIETLEEAVTLmSEEKNNGRmNKYAARALLARIYLYHDDNRKAFDLADQLIKDADTSGSYALYPHEKYVAAWSVEAKFGSESFFEIANSVDDTPGRDSWGYLLNWYGYQKGFVTQKYAEQmLADPGDVRGHLLEENKYAGKTVWWLYKLRGTDLKTAPLECNNVVLRLSEVYLIAAEAGCKLGGDAAVQGLGYLNEIVKRGNPDNEVTmADYTLDRVLDERSKELVGEGHRFFDLLRNGKTIVRKGGYHLPSVDEEVDWDFYKCVLPIPEDQFIFSPEmEQNPGYPK 479
                                    45       |55       |65   |    75        85  |     95       105       115       125       135    |  145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395     | 405       415       425       435       445       455       465     | 475    
                                            53-MSE    63-MSE |    |            88-MSE                                             140-MSE                                                         204-MSE  213-MSE                                                                                             313-MSE                                                                                 401-MSE                                                               471-MSE    
                                                            69-MSE|                                                                                                                                                                                                                                                                                                                                                                                                                     
                                                                 74-MSE
   Legend:   → Mismatch (orange background)
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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 3MYV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: TPR (230)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3MYV)

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