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(-) Description

Title :  CRYSTAL STRUCTURE OF A PUTATIVE GLYCOSIDASE (BT_4094) FROM BACTEROIDES THETAIOTAOMICRON VPI-5482 AT 2.30 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  21 Mar 11  (Deposition) - 13 Apr 11  (Release) - 13 Apr 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  5-Bladed Beta Propeller Fold, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi- Biology, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of A Putative Glycosidase (Bt_4094) From Bacteroides Thetaiotaomicron Vpi-5482 At 2. 30 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE GLYCOSIDASE
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidSPEEDET
    Expression System StrainHK100
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneBT_4094
    Organism ScientificBACTEROIDES THETAIOTAOMICRON
    Organism Taxid226186
    StrainVPI-5482

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A   
Biological Unit 2 (1x) B  
Biological Unit 3 (1x)  C 
Biological Unit 4 (1x)   D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 44)

Asymmetric Unit (2, 44)
No.NameCountTypeFull Name
1EDO20Ligand/Ion1,2-ETHANEDIOL
2MSE24Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 13)
No.NameCountTypeFull Name
1EDO7Ligand/Ion1,2-ETHANEDIOL
2MSE6Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 10)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2MSE6Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (2, 12)
No.NameCountTypeFull Name
1EDO6Ligand/Ion1,2-ETHANEDIOL
2MSE6Mod. Amino AcidSELENOMETHIONINE
Biological Unit 4 (2, 9)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
2MSE6Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:74 , TYR A:303 , TYR A:339 , PHE A:345 , ASP A:364 , HOH A:1246 , HOH A:1426BINDING SITE FOR RESIDUE EDO A 382
02AC2SOFTWAREILE A:255 , THR A:256 , ARG A:321 , HOH A:522 , HOH A:1213BINDING SITE FOR RESIDUE EDO A 383
03AC3SOFTWAREPRO A:325 , PHE A:326BINDING SITE FOR RESIDUE EDO A 384
04AC4SOFTWAREHOH A:972BINDING SITE FOR RESIDUE EDO A 385
05AC5SOFTWAREGLU A:141 , TRP A:160 , ALA A:165 , PHE A:197 , LYS A:199BINDING SITE FOR RESIDUE EDO A 388
06AC6SOFTWAREASN A:288 , LYS A:289 , GLY A:291 , TYR A:298 , HOH A:1063BINDING SITE FOR RESIDUE EDO A 389
07AC7SOFTWAREALA A:77 , THR A:78 , VAL A:145 , GLN A:212 , PRO A:272 , LEU A:349 , HOH A:734 , HOH A:990 , HOH A:1140 , HOH A:1516BINDING SITE FOR RESIDUE EDO A 392
08AC8SOFTWAREASN B:74 , TYR B:303 , ASP B:364 , HOH B:961 , HOH B:1418BINDING SITE FOR RESIDUE EDO B 379
09AC9SOFTWAREGLU B:141 , TRP B:160 , LYS B:199 , HOH B:478 , HOH B:1255 , HOH B:1329BINDING SITE FOR RESIDUE EDO B 390
10BC1SOFTWAREVAL B:254 , THR B:256 , ARG B:321 , HOH B:610BINDING SITE FOR RESIDUE EDO B 391
11BC2SOFTWAREGLY A:43 , LYS B:132 , GLU B:133 , TRP B:136 , HOH B:460BINDING SITE FOR RESIDUE EDO B 395
12BC3SOFTWARELYS C:199 , EDO C:380 , EDO C:386 , HOH C:413 , HOH C:427 , HOH C:878 , HOH C:1146BINDING SITE FOR RESIDUE EDO C 378
13BC4SOFTWAREASN C:74 , TYR C:303 , TYR C:339 , ASP C:364 , EDO C:378 , HOH C:878 , HOH C:1181BINDING SITE FOR RESIDUE EDO C 380
14BC5SOFTWAREVAL C:254 , ILE C:255 , THR C:256 , ARG C:321 , HOH C:1269BINDING SITE FOR RESIDUE EDO C 381
15BC6SOFTWAREGLU C:141 , TRP C:160 , LYS C:199 , EDO C:378 , HOH C:1146BINDING SITE FOR RESIDUE EDO C 386
16BC7SOFTWAREALA C:77 , THR C:78 , VAL C:145 , ALA C:146 , GLN C:212 , PRO C:272 , LEU C:349 , HOH C:1512 , HOH C:1513 , HOH C:1529BINDING SITE FOR RESIDUE EDO C 387
17BC8SOFTWARESER C:70 , ASP C:92 , ASN C:93 , ALA C:95 , VAL C:96 , HOH C:1298BINDING SITE FOR RESIDUE EDO C 393
18BC9SOFTWAREASN D:74 , TYR D:303 , PHE D:345 , ASP D:364 , HOH D:484 , HOH D:1315BINDING SITE FOR RESIDUE EDO D 394
19CC1SOFTWAREGLU D:141 , TRP D:160 , ALA D:165 , LYS D:199BINDING SITE FOR RESIDUE EDO D 396
20CC2SOFTWARETYR D:109 , MSE D:119 , HOH D:1170BINDING SITE FOR RESIDUE EDO D 397

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3R67)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Asn A:45 -Pro A:46
2Trp A:136 -Pro A:137
3Asn B:45 -Pro B:46
4Trp B:136 -Pro B:137
5Asn C:45 -Pro C:46
6Trp C:136 -Pro C:137
7Asn D:45 -Pro D:46
8Trp D:136 -Pro D:137

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3R67)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3R67)

(-) Exons   (0, 0)

(no "Exon" information available for 3R67)

(-) 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:349
 aligned with Q8A0C7_BACTN | Q8A0C7 from UniProtKB/TrEMBL  Length:377

    Alignment length:349
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367         
         Q8A0C7_BACTN    28 SEFPDWAWADFQRPEGINPIVSPDTTTVFYCPMRQDSVAWESSDTFNPAATIYDGKVVVLYRAEDNSAVGIGSRTSRLGYAYSDDGLHFNRMTVPVFYPADDNQKELEWPGGCEDPRVAVTEDGLYVMLYTQWNRKQARLAVATSRDLQIWEKYGPAFAKAYGGRFFDEFSKSASIVTKLVDGKQVIAKIDGKYWMYWGEKFVNVATSTDLINWEPMLDEKGDFLKVITPREGKFDSDLTECGPPAIMTDKGILLLYNGKNKSGAEGDTLYTANSYCAGQALFDAKDPTKLIDRLDKPFYIPESDFEKSGQYPAGTVFIEGLVFHNQKWYLYYGCADSRVAVAVYDPFK 376
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......................................................................................................hhhhhh..................................................hhhhhh..........................................................................................................................................hhhhhh........................................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r67 A  28 SEFPDWAWADFQRPEGINPIVSPDTTTVFYCPmRQDSVAWESSDTFNPAATIYDGKVVVLYRAEDNSAVGIGSRTSRLGYAYSDDGLHFNRmTVPVFYPADDNQKELEWPGGCEDPRVAVTEDGLYVmLYTQWNRKQARLAVATSRDLQIWEKYGPAFAKAYGGRFFDEFSKSASIVTKLVDGKQVIAKIDGKYWmYWGEKFVNVATSTDLINWEPmLDEKGDFLKVITPREGKFDSDLTECGPPAImTDKGILLLYNGKNKSGAEGDTLYTANSYCAGQALFDAKDPTKLIDRLDKPFYIPESDFEKSGQYPAGTVFIEGLVFHNQKWYLYYGCADSRVAVAVYDPFK 376
                                    37        47        57  |     67        77        87        97       107       117 |     127       137       147       157       167       177       187       197       207       217     | 227       237      |247       257       267       277       287       297       307       317       327       337       347       357       367         
                                                           60-MSE                                                    119-MSE                             155-MSE                                                             223-MSE              244-MSE                        275-MSE                                                                                                 

Chain B from PDB  Type:PROTEIN  Length:349
 aligned with Q8A0C7_BACTN | Q8A0C7 from UniProtKB/TrEMBL  Length:377

    Alignment length:349
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367         
         Q8A0C7_BACTN    28 SEFPDWAWADFQRPEGINPIVSPDTTTVFYCPMRQDSVAWESSDTFNPAATIYDGKVVVLYRAEDNSAVGIGSRTSRLGYAYSDDGLHFNRMTVPVFYPADDNQKELEWPGGCEDPRVAVTEDGLYVMLYTQWNRKQARLAVATSRDLQIWEKYGPAFAKAYGGRFFDEFSKSASIVTKLVDGKQVIAKIDGKYWMYWGEKFVNVATSTDLINWEPMLDEKGDFLKVITPREGKFDSDLTECGPPAIMTDKGILLLYNGKNKSGAEGDTLYTANSYCAGQALFDAKDPTKLIDRLDKPFYIPESDFEKSGQYPAGTVFIEGLVFHNQKWYLYYGCADSRVAVAVYDPFK 376
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......................................................................................................hhhhhh..................................................hhhhhh.................................................................................................hhhhh....................................hhhhhh........................................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r67 B  28 SEFPDWAWADFQRPEGINPIVSPDTTTVFYCPmRQDSVAWESSDTFNPAATIYDGKVVVLYRAEDNSAVGIGSRTSRLGYAYSDDGLHFNRmTVPVFYPADDNQKELEWPGGCEDPRVAVTEDGLYVmLYTQWNRKQARLAVATSRDLQIWEKYGPAFAKAYGGRFFDEFSKSASIVTKLVDGKQVIAKIDGKYWmYWGEKFVNVATSTDLINWEPmLDEKGDFLKVITPREGKFDSDLTECGPPAImTDKGILLLYNGKNKSGAEGDTLYTANSYCAGQALFDAKDPTKLIDRLDKPFYIPESDFEKSGQYPAGTVFIEGLVFHNQKWYLYYGCADSRVAVAVYDPFK 376
                                    37        47        57  |     67        77        87        97       107       117 |     127       137       147       157       167       177       187       197       207       217     | 227       237      |247       257       267       277       287       297       307       317       327       337       347       357       367         
                                                           60-MSE                                                    119-MSE                             155-MSE                                                             223-MSE              244-MSE                        275-MSE                                                                                                 

Chain C from PDB  Type:PROTEIN  Length:349
 aligned with Q8A0C7_BACTN | Q8A0C7 from UniProtKB/TrEMBL  Length:377

    Alignment length:349
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367         
         Q8A0C7_BACTN    28 SEFPDWAWADFQRPEGINPIVSPDTTTVFYCPMRQDSVAWESSDTFNPAATIYDGKVVVLYRAEDNSAVGIGSRTSRLGYAYSDDGLHFNRMTVPVFYPADDNQKELEWPGGCEDPRVAVTEDGLYVMLYTQWNRKQARLAVATSRDLQIWEKYGPAFAKAYGGRFFDEFSKSASIVTKLVDGKQVIAKIDGKYWMYWGEKFVNVATSTDLINWEPMLDEKGDFLKVITPREGKFDSDLTECGPPAIMTDKGILLLYNGKNKSGAEGDTLYTANSYCAGQALFDAKDPTKLIDRLDKPFYIPESDFEKSGQYPAGTVFIEGLVFHNQKWYLYYGCADSRVAVAVYDPFK 376
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......................................................................................................hhhhhh..................................................hhhhhh.................................................................................................hhhhh....................................hhhhhh........................................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r67 C  28 SEFPDWAWADFQRPEGINPIVSPDTTTVFYCPmRQDSVAWESSDTFNPAATIYDGKVVVLYRAEDNSAVGIGSRTSRLGYAYSDDGLHFNRmTVPVFYPADDNQKELEWPGGCEDPRVAVTEDGLYVmLYTQWNRKQARLAVATSRDLQIWEKYGPAFAKAYGGRFFDEFSKSASIVTKLVDGKQVIAKIDGKYWmYWGEKFVNVATSTDLINWEPmLDEKGDFLKVITPREGKFDSDLTECGPPAImTDKGILLLYNGKNKSGAEGDTLYTANSYCAGQALFDAKDPTKLIDRLDKPFYIPESDFEKSGQYPAGTVFIEGLVFHNQKWYLYYGCADSRVAVAVYDPFK 376
                                    37        47        57  |     67        77        87        97       107       117 |     127       137       147       157       167       177       187       197       207       217     | 227       237      |247       257       267       277       287       297       307       317       327       337       347       357       367         
                                                           60-MSE                                                    119-MSE                             155-MSE                                                             223-MSE              244-MSE                        275-MSE                                                                                                 

Chain D from PDB  Type:PROTEIN  Length:348
 aligned with Q8A0C7_BACTN | Q8A0C7 from UniProtKB/TrEMBL  Length:377

    Alignment length:348
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368        
         Q8A0C7_BACTN    29 EFPDWAWADFQRPEGINPIVSPDTTTVFYCPMRQDSVAWESSDTFNPAATIYDGKVVVLYRAEDNSAVGIGSRTSRLGYAYSDDGLHFNRMTVPVFYPADDNQKELEWPGGCEDPRVAVTEDGLYVMLYTQWNRKQARLAVATSRDLQIWEKYGPAFAKAYGGRFFDEFSKSASIVTKLVDGKQVIAKIDGKYWMYWGEKFVNVATSTDLINWEPMLDEKGDFLKVITPREGKFDSDLTECGPPAIMTDKGILLLYNGKNKSGAEGDTLYTANSYCAGQALFDAKDPTKLIDRLDKPFYIPESDFEKSGQYPAGTVFIEGLVFHNQKWYLYYGCADSRVAVAVYDPFK 376
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ----------DUF377-3r67D01 D:39-376                                                                                                                                                                                                                                                                                                                            Pfam domains (1)
           Pfam domains (2) ----------DUF377-3r67D02 D:39-376                                                                                                                                                                                                                                                                                                                            Pfam domains (2)
           Pfam domains (3) ----------DUF377-3r67D03 D:39-376                                                                                                                                                                                                                                                                                                                            Pfam domains (3)
           Pfam domains (4) ----------DUF377-3r67D04 D:39-376                                                                                                                                                                                                                                                                                                                            Pfam domains (4)
         Sec.struct. author ......................................................................................................hhhhhh..................................................hhhhhh.................................................................................................hhhhh....................................hhhhh......................................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3r67 D  29 EFPDWAWADFQRPEGINPIVSPDTTTVFYCPmRQDSVAWESSDTFNPAATIYDGKVVVLYRAEDNSAVGIGSRTSRLGYAYSDDGLHFNRmTVPVFYPADDNQKELEWPGGCEDPRVAVTEDGLYVmLYTQWNRKQARLAVATSRDLQIWEKYGPAFAKAYGGRFFDEFSKSASIVTKLVDGKQVIAKIDGKYWmYWGEKFVNVATSTDLINWEPmLDEKGDFLKVITPREGKFDSDLTECGPPAImTDKGILLLYNGKNKSGAEGDTLYTANSYCAGQALFDAKDPTKLIDRLDKPFYIPESDFEKSGQYPAGTVFIEGLVFHNQKWYLYYGCADSRVAVAVYDPFK 376
                                    38        48        58 |      68        78        88        98       108       118|      128       138       148      |158       168       178       188       198       208       218    |  228       238     | 248       258       268      |278       288       298       308       318       328       338       348       358       368        
                                                          60-MSE                                                    119-MSE                             155-MSE                                                             223-MSE              244-MSE                        275-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 3R67)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3R67)

(-) Pfam Domains  (1, 4)

Asymmetric Unit

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q8A0C7_BACTN | Q8A0C7)
molecular function
    GO:0016798    hydrolase activity, acting on glycosyl bonds    Catalysis of the hydrolysis of any glycosyl bond.
biological process
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

(no "Entries Sharing at Least One Protein Chain" available for 3R67)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3R67)