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(-) Description

Title :  CRYSTAL STRUCTURE OF SUSD SUPERFAMILY PROTEIN (YP_001297730.1) FROM BACTEROIDES VULGATUS ATCC 8482 AT 1.55 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  04 Sep 09  (Deposition) - 22 Sep 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Yp_001297730. 1, Susd Superfamily Protein, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Ragb, Susd And Hypothetical Proteins, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Susd Superfamily Protein (Yp_001297730. 1) From Bacteroides Vulgatus Atcc 8482 At 1. 5 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - SUSD SUPERFAMILY PROTEIN
    Atcc: 8482 / DSM 1447 / NCTC 11154
    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 34-513
    Gene: BVU_0390, YP_001297730.1
    Organism Scientific: BACTEROIDES VULGATUS ATCC 8482
    Organism Taxid: 435590
    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, 38)

Asymmetric Unit (4, 38)
No.NameCountTypeFull Name
1CA11Ligand/IonCALCIUM ION
2CL11Ligand/IonCHLORIDE ION
3EDO4Ligand/Ion1,2-ETHANEDIOL
4MSE12Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3EDO2Ligand/Ion1,2-ETHANEDIOL
4MSE6Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 8)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3EDO2Ligand/Ion1,2-ETHANEDIOL
4MSE6Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (26, 26)

Asymmetric Unit (26, 26)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:471 , HOH A:520 , HOH A:563 , HOH A:701 , HOH A:703 , HOH A:882 , HOH A:959BINDING SITE FOR RESIDUE CA A 2
02AC2SOFTWARELEU A:200 , GLN A:211 , HOH A:824 , HOH A:868 , HOH A:869 , HOH A:1136 , HOH A:1286BINDING SITE FOR RESIDUE CA A 5
03AC3SOFTWARESER A:102 , HOH A:559 , HOH A:630 , HOH A:712 , HOH A:735 , HOH A:1126 , HOH A:1131 , HOH A:1295BINDING SITE FOR RESIDUE CA A 6
04AC4SOFTWAREASP A:257 , GLU A:260 , PHE A:384 , HOH A:553 , HOH A:562 , HOH B:558BINDING SITE FOR RESIDUE CA A 7
05AC5SOFTWARETHR A:91 , ASN A:97 , SER A:98 , ASN A:101 , HOH A:825 , HOH A:879BINDING SITE FOR RESIDUE CL A 12
06AC6SOFTWARECL A:20 , ASN A:261 , ILE B:206 , HOH B:1017BINDING SITE FOR RESIDUE CL A 14
07AC7SOFTWAREGLY A:463 , LEU A:465 , GLU A:466BINDING SITE FOR RESIDUE CL A 17
08AC8SOFTWAREGLN A:229 , LYS A:406 , HOH B:840 , HOH B:1033BINDING SITE FOR RESIDUE CL A 19
09AC9SOFTWARECL A:14 , ILE A:206 , HOH A:673 , ASN B:261BINDING SITE FOR RESIDUE CL A 20
10BC1SOFTWAREARG A:94 , ASN A:479BINDING SITE FOR RESIDUE CL A 21
11BC2SOFTWARETHR A:362 , TYR A:363 , HOH A:880 , HOH A:1179BINDING SITE FOR RESIDUE CL A 22
12BC3SOFTWARETYR A:112 , ARG A:165 , GLU A:500 , HOH A:676 , HOH A:1234BINDING SITE FOR RESIDUE EDO A 23
13BC4SOFTWAREGLU A:249 , TYR A:331 , HOH A:1350BINDING SITE FOR RESIDUE EDO A 25
14BC5SOFTWAREHOH A:515 , ASP B:257 , GLU B:260 , PHE B:384 , HOH B:514 , HOH B:585BINDING SITE FOR RESIDUE CA B 1
15BC6SOFTWAREEDO B:26 , GLU B:466 , HOH B:767 , HOH B:828 , HOH B:841 , HOH B:869 , HOH B:881BINDING SITE FOR RESIDUE CA B 3
16BC7SOFTWARELEU B:200 , GLN B:211 , HOH B:590 , HOH B:694 , HOH B:958 , HOH B:983 , HOH B:1236BINDING SITE FOR RESIDUE CA B 4
17BC8SOFTWARESER B:102 , HOH B:653 , HOH B:718 , HOH B:777 , HOH B:803 , HOH B:940 , HOH B:1133 , HOH B:1140BINDING SITE FOR RESIDUE CA B 8
18BC9SOFTWAREHOH B:550 , HOH B:804 , HOH B:824 , HOH B:849 , HOH B:926 , HOH B:1045 , HOH B:1071BINDING SITE FOR RESIDUE CA B 9
19CC1SOFTWAREGLY B:327 , ASP B:486 , HOH B:928 , HOH B:1108 , HOH B:1164 , HOH B:1377BINDING SITE FOR RESIDUE CA B 10
20CC2SOFTWARETHR B:471 , HOH B:769 , HOH B:1279 , HOH B:1306 , HOH B:1471BINDING SITE FOR RESIDUE CA B 11
21CC3SOFTWAREGLY B:463 , LEU B:465 , GLU B:466BINDING SITE FOR RESIDUE CL B 13
22CC4SOFTWARETHR B:91 , ASN B:97 , SER B:98 , ASN B:101 , HOH B:705 , HOH B:761 , HOH B:951BINDING SITE FOR RESIDUE CL B 15
23CC5SOFTWARETHR B:362 , TYR B:363 , HOH B:692 , HOH B:1190BINDING SITE FOR RESIDUE CL B 16
24CC6SOFTWAREARG B:94 , ASN B:479 , HOH B:1269BINDING SITE FOR RESIDUE CL B 18
25CC7SOFTWAREGLU B:249 , HOH B:1396BINDING SITE FOR RESIDUE EDO B 24
26CC8SOFTWARECA B:3 , GLU B:466 , ASP B:486 , ASN B:487 , HOH B:696 , HOH B:767 , HOH B:869 , HOH B:881 , HOH B:955BINDING SITE FOR RESIDUE EDO B 26

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3JQ1)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Asn A:241 -Pro A:242
2Ala A:379 -Pro A:380
3Asn B:241 -Pro B:242
4Ala B:379 -Pro B:380

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3JQ1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3JQ1)

(-) Exons   (0, 0)

(no "Exon" information available for 3JQ1)

(-) 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:462
 aligned with A6KXE4_BACV8 | A6KXE4 from UniProtKB/TrEMBL  Length:513

    Alignment length:477
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       
         A6KXE4_BACV8    37 TFWKDETDFNLALTSCYTPLKNALNGGYYGTRGVMLRIARADEVDFRNDISDVYTVNRFTNSNTNSLTQGMFYQFYNALYRTNSIMQKLEEKKEQFSTDFQNSVKGECLFIRGFYLFQLAKEFKDAPLRLTASQSPSTFPLAKSSQADIWAQAKEDLKTAASLLPITNKIGKPTQGAAYAALGKIYVYEENWQEAINVLEPLTQNPYTYKLVEDFNWNFDDTHENNAESIFELLIEDVGGTDLWGDGENINSTQSNTRPKEYAAAEVGGWYEANPTQQIMDIFWKEKDKDGNFDYRARCSVAWDYEGCTYYQRPFREVFAQDKWKTYWILKYQNWKTQKDEPAPPKSFINERAIRYADVLLMLAEAYMNKGALDTSIGYINQIRRRANLNDYSGPITKEGVFEDLVHQRAIEFFVEGERFYDLRRWGLLEQTLKTCDDTRYKNYQTGKSDNINKFNYFPIPAKELDTNPLCTPSEGW 513
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhh....eee...hhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....................hhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.........hhhhhhh........eeeee.....-----.----------..hhhhhhhhhhhh....eeehhhhhhhhhh........hhhhhhhee......ee..eehhhhhhhhhh...ee.....................eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhh....hhhhhhhhh.hhhhhhhh.hhhhhhhhhh.ee..ee.hhh...hhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jq1 A  37 TFWKDETDFNLALTSCYTPLKNALNGGYYGTRGVmLRIARADEVDFRNDISDVYTVNRFTNSNTNSLTQGmFYQFYNALYRTNSImQKLEEKKEQFSTDFQNSVKGECLFIRGFYLFQLAKEFKDAPLRLTASQSPSTFPLAKSSQADIWAQAKEDLKTAASLLPITNKIGKPTQGAAYAALGKIYVYEENWQEAINVLEPLTQNPYTYKLVEDFNWNFDDTHENNAESIFELLIEDV-----W----------SNTRPKEYAAAEVGGWYEANPTQQImDIFWKEKDKDGNFDYRARCSVAWDYEGCTYYQRPFREVFAQDKWKTYWILKYQNWKTQKDEPAPPKSFINERAIRYADVLLmLAEAYmNKGALDTSIGYINQIRRRANLNDYSGPITKEGVFEDLVHQRAIEFFVEGERFYDLRRWGLLEQTLKTCDDTRYKNYQTGKSDNINKFNYFPIPAKELDTNPLCTPSEGW 513
                                    46        56        66    |   76        86        96       106|      116     | 126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       | -   |     -    |  296       306       316       326       336       346       356       366       376       386       396 |     406       416       426       436       446       456       466       476       486       496       506       
                                                             71-MSE                             107-MSE        122-MSE                                                                                                                                                 274   280        291                      316-MSE                                                                           398-MSE |                                                                                                             
                                                                                                                                                                                                                                                                                                                                                                                                         404-MSE                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:464
 aligned with A6KXE4_BACV8 | A6KXE4 from UniProtKB/TrEMBL  Length:513

    Alignment length:477
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       
         A6KXE4_BACV8    37 TFWKDETDFNLALTSCYTPLKNALNGGYYGTRGVMLRIARADEVDFRNDISDVYTVNRFTNSNTNSLTQGMFYQFYNALYRTNSIMQKLEEKKEQFSTDFQNSVKGECLFIRGFYLFQLAKEFKDAPLRLTASQSPSTFPLAKSSQADIWAQAKEDLKTAASLLPITNKIGKPTQGAAYAALGKIYVYEENWQEAINVLEPLTQNPYTYKLVEDFNWNFDDTHENNAESIFELLIEDVGGTDLWGDGENINSTQSNTRPKEYAAAEVGGWYEANPTQQIMDIFWKEKDKDGNFDYRARCSVAWDYEGCTYYQRPFREVFAQDKWKTYWILKYQNWKTQKDEPAPPKSFINERAIRYADVLLMLAEAYMNKGALDTSIGYINQIRRRANLNDYSGPITKEGVFEDLVHQRAIEFFVEGERFYDLRRWGLLEQTLKTCDDTRYKNYQTGKSDNINKFNYFPIPAKELDTNPLCTPSEGW 513
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) SusD-like_3-3jq1B03 B:37-223                                                                                                                                                               ---------------------------------------SusD-3jq1B01              B:263-513                                                                                                                                                                                                                         Pfam domains (1)
           Pfam domains (2) SusD-like_3-3jq1B04 B:37-223                                                                                                                                                               ---------------------------------------SusD-3jq1B02              B:263-513                                                                                                                                                                                                                         Pfam domains (2)
         Sec.struct. author ....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhh....eee...hhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....................hhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.........hhhhhhh........eeeee.....-----.--------....hhhhhhhhhhhh....eeehhhhhhhhhh........hhhhhhhee......ee..eehhhhhhhhhh...ee.....................eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhh....hhhhhhhhh.hhhhhhhhhhhhhhhhhhh.ee..ee.hhh...hhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jq1 B  37 TFWKDETDFNLALTSCYTPLKNALNGGYYGTRGVmLRIARADEVDFRNDISDVYTVNRFTNSNTNSLTQGmFYQFYNALYRTNSImQKLEEKKEQFSTDFQNSVKGECLFIRGFYLFQLAKEFKDAPLRLTASQSPSTFPLAKSSQADIWAQAKEDLKTAASLLPITNKIGKPTQGAAYAALGKIYVYEENWQEAINVLEPLTQNPYTYKLVEDFNWNFDDTHENNAESIFELLIEDV-----W--------TQSNTRPKEYAAAEVGGWYEANPTQQImDIFWKEKDKDGNFDYRARCSVAWDYEGCTYYQRPFREVFAQDKWKTYWILKYQNWKTQKDEPAPPKSFINERAIRYADVLLmLAEAYmNKGALDTSIGYINQIRRRANLNDYSGPITKEGVFEDLVHQRAIEFFVEGERFYDLRRWGLLEQTLKTCDDTRYKNYQTGKSDNINKFNYFPIPAKELDTNPLCTPSEGW 513
                                    46        56        66    |   76        86        96       106|      116     | 126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       | -   |     -  |    296       306       316       326       336       346       356       366       376       386       396 |     406       416       426       436       446       456       466       476       486       496       506       
                                                             71-MSE                             107-MSE        122-MSE                                                                                                                                                 274   280      289                        316-MSE                                                                           398-MSE |                                                                                                             
                                                                                                                                                                                                                                                                                                                                                                                                         404-MSE
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  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 3JQ1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3JQ1)

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: TPR (230)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (A6KXE4_BACV8 | A6KXE4)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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