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(-) Description

Title :  THE CRYSTAL STRUCTURE OF A POSSIBLE METAL-DEPENDENT HYDROLASE FROM VEILLONELLA PARVULA DSM 2008
 
Authors :  K. Tan, N. Marshall, S. Clancy, A. Joachimiak, Midwest Center For St Genomics (Mcsg)
Date :  26 Apr 11  (Deposition) - 11 May 11  (Release) - 11 May 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.49
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Structural Genomics, Psi-Biology, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Tan, N. Marshall, S. Clancy, A. Joachimiak
The Crystal Structure Of A Possible Metal-Dependent Hydrolase From Veillonella Parvula Dsm 2008
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - POSSIBLE METAL-DEPENDENT HYDROLASE
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: VPAR_0210
    Organism Scientific: VEILLONELLA PARVULA
    Organism Taxid: 479436
    Strain: DSM 2008

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A  D
Biological Unit 2 (1x):  BC 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 48)

Asymmetric Unit (2, 48)
No.NameCountTypeFull Name
1MSE40Mod. Amino AcidSELENOMETHIONINE
2ZN8Ligand/IonZINC ION
Biological Unit 1 (1, 20)
No.NameCountTypeFull Name
1MSE20Mod. Amino AcidSELENOMETHIONINE
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 20)
No.NameCountTypeFull Name
1MSE20Mod. Amino AcidSELENOMETHIONINE
2ZN-1Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:69 , HIS A:71 , HIS A:129 , ASP A:165 , ZN A:302 , HOH A:1177BINDING SITE FOR RESIDUE ZN A 301
2AC2SOFTWAREASP A:73 , HIS A:74 , ASP A:165 , HIS A:223 , ZN A:301 , HOH A:521 , HOH A:1177BINDING SITE FOR RESIDUE ZN A 302
3AC3SOFTWAREHIS B:69 , HIS B:71 , HIS B:129 , ASP B:165 , ZN B:302 , HOH B:1178BINDING SITE FOR RESIDUE ZN B 301
4AC4SOFTWAREASP B:73 , HIS B:74 , ASP B:165 , HIS B:223 , ZN B:301 , HOH B:520 , HOH B:1178BINDING SITE FOR RESIDUE ZN B 302
5AC5SOFTWAREHIS C:69 , HIS C:71 , HIS C:129 , ASP C:165 , ZN C:302 , HOH C:1175BINDING SITE FOR RESIDUE ZN C 301
6AC6SOFTWAREASP C:73 , HIS C:74 , ASP C:165 , HIS C:223 , HOH C:275 , ZN C:301 , HOH C:1175BINDING SITE FOR RESIDUE ZN C 302
7AC7SOFTWAREHIS D:69 , HIS D:71 , HIS D:129 , ASP D:165 , ZN D:302 , HOH D:1176BINDING SITE FOR RESIDUE ZN D 301
8AC8SOFTWAREASP D:73 , HIS D:74 , ASP D:165 , HIS D:223 , ZN D:301 , HOH D:313 , HOH D:1176BINDING SITE FOR RESIDUE ZN D 302

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Mse A:46 -Pro A:47
2Mse B:46 -Pro B:47
3Mse C:46 -Pro C:47
4Mse D:46 -Pro D:47

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3RPC)

(-) 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:262
 aligned with D1BQT4_VEIPT | D1BQT4 from UniProtKB/TrEMBL  Length:261

    Alignment length:262
                             1                                                                                                                                                                                                                                                                    
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259  
         D1BQT4_VEIPT     - -MTQYTHIRNATGKLTIKNTTFLIDPFLAPKDTYPGFEGTFNYQQRMPMVDLPLSMDDLLSNVTAVVVTHTHLDHWDDTAINSIPKSLPIFVQNTADKELITSQGFIDVRIIFESLEFNGITLRKTGGSHGTVEMYANPVLAPLAGDAMGVIFEAADEPTVYLVGDTVWTSDVEKALLRFDPNVIIMNTGYAQILGFEDSIIMGTKDIGRMVVRKPEAKIIAVHMDTVNHTATSRKDVRKFIKGNNIESHVAVPEDGETITL 261
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee..eeeeee..eeeee..............................hhhhhhh...eee....hhhhhhhhhhhhh.....eee.hhhhhhhhhhh....eee...eeee..eeeeee.....hhhhhh..hhhhhhh...eeeee......eee......hhhhhhhhhhhh..eeeee...............hhhhhhhhhhhh...eeeee..........hhhhhhhhhhhh.....ee......eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rpc A   0 AmTQYTHIRNATGKLTIKNTTFLIDPFLAPKDTYPGFEGTFNYQQRmPmVDLPLSmDDLLSNVTAVVVTHTHLDHWDDTAINSIPKSLPIFVQNTADKELITSQGFIDVRIIFESLEFNGITLRKTGGSHGTVEmYANPVLAPLAGDAmGVIFEAADEPTVYLVGDTVWTSDVEKALLRFDPNVIImNTGYAQILGFEDSIImGTKDIGRmVVRKPEAKIIAVHmDTVNHTATSRKDVRKFIKGNNIESHVAVPEDGETITL 261
                             |       9        19        29        39      | 49     |  59        69        79        89        99       109       119       129    |  139       149       159       169       179      |189       199  |    209|      219    |  229       239       249       259  
                             |                                           46-MSE   55-MSE                                                                        134-MSE       148-MSE                               186-MSE         202-MSE 210-MSE       224-MSE                                 
                             1-MSE                                         48-MSE                                                                                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:262
 aligned with D1BQT4_VEIPT | D1BQT4 from UniProtKB/TrEMBL  Length:261

    Alignment length:262
                             1                                                                                                                                                                                                                                                                    
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259  
         D1BQT4_VEIPT     - -MTQYTHIRNATGKLTIKNTTFLIDPFLAPKDTYPGFEGTFNYQQRMPMVDLPLSMDDLLSNVTAVVVTHTHLDHWDDTAINSIPKSLPIFVQNTADKELITSQGFIDVRIIFESLEFNGITLRKTGGSHGTVEMYANPVLAPLAGDAMGVIFEAADEPTVYLVGDTVWTSDVEKALLRFDPNVIIMNTGYAQILGFEDSIIMGTKDIGRMVVRKPEAKIIAVHMDTVNHTATSRKDVRKFIKGNNIESHVAVPEDGETITL 261
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee..eeeeee..eeeee..............................hhhhhhh...eee....hhhhhhhhhhhhh.....eee.hhhhhhhhhhh....eee...eeee..eeeeee.....hhhhhh..hhhhhhh...eeeee......eee......hhhhhhhhhhhh..eeeee...............hhhhhhhhhhhh...eeeee..........hhhhhhhhhhhh.hhh.ee......eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rpc B   0 AmTQYTHIRNATGKLTIKNTTFLIDPFLAPKDTYPGFEGTFNYQQRmPmVDLPLSmDDLLSNVTAVVVTHTHLDHWDDTAINSIPKSLPIFVQNTADKELITSQGFIDVRIIFESLEFNGITLRKTGGSHGTVEmYANPVLAPLAGDAmGVIFEAADEPTVYLVGDTVWTSDVEKALLRFDPNVIImNTGYAQILGFEDSIImGTKDIGRmVVRKPEAKIIAVHmDTVNHTATSRKDVRKFIKGNNIESHVAVPEDGETITL 261
                             |       9        19        29        39      | 49     |  59        69        79        89        99       109       119       129    |  139       149       159       169       179      |189       199  |    209|      219    |  229       239       249       259  
                             1-MSE                                       46-MSE   55-MSE                                                                        134-MSE       148-MSE                               186-MSE         202-MSE 210-MSE       224-MSE                                 
                                                                           48-MSE                                                                                                                                                                                                                 


Chain C from PDB  Type:PROTEIN  Length:262
 aligned with D1BQT4_VEIPT | D1BQT4 from UniProtKB/TrEMBL  Length:261

    Alignment length:262
                             1                                                                                                                                                                                                                                                                    
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259  
         D1BQT4_VEIPT     - -MTQYTHIRNATGKLTIKNTTFLIDPFLAPKDTYPGFEGTFNYQQRMPMVDLPLSMDDLLSNVTAVVVTHTHLDHWDDTAINSIPKSLPIFVQNTADKELITSQGFIDVRIIFESLEFNGITLRKTGGSHGTVEMYANPVLAPLAGDAMGVIFEAADEPTVYLVGDTVWTSDVEKALLRFDPNVIIMNTGYAQILGFEDSIIMGTKDIGRMVVRKPEAKIIAVHMDTVNHTATSRKDVRKFIKGNNIESHVAVPEDGETITL 261
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee..eeeeee..eeeee..............................hhhhhhh...eee....hhhhhhhhhhhhh.....eee.hhhhhhhhhhh....eee...eeee..eeeeee.....hhhhhh..hhhhhhh...eeeee......eee......hhhhhhhhhhhh..eeeee...............hhhhhhhhhhhh...eeeee..........hhhhhhhhhhhh.hhh.ee......eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rpc C   0 AmTQYTHIRNATGKLTIKNTTFLIDPFLAPKDTYPGFEGTFNYQQRmPmVDLPLSmDDLLSNVTAVVVTHTHLDHWDDTAINSIPKSLPIFVQNTADKELITSQGFIDVRIIFESLEFNGITLRKTGGSHGTVEmYANPVLAPLAGDAmGVIFEAADEPTVYLVGDTVWTSDVEKALLRFDPNVIImNTGYAQILGFEDSIImGTKDIGRmVVRKPEAKIIAVHmDTVNHTATSRKDVRKFIKGNNIESHVAVPEDGETITL 261
                             |       9        19        29        39      | 49     |  59        69        79        89        99       109       119       129    |  139       149       159       169       179      |189       199  |    209|      219    |  229       239       249       259  
                             1-MSE                                       46-MSE   55-MSE                                                                        134-MSE       148-MSE                               186-MSE         202-MSE 210-MSE       224-MSE                                 
                                                                           48-MSE                                                                                                                                                                                                                 


Chain D from PDB  Type:PROTEIN  Length:262
 aligned with D1BQT4_VEIPT | D1BQT4 from UniProtKB/TrEMBL  Length:261

    Alignment length:262
                             1                                                                                                                                                                                                                                                                    
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259  
         D1BQT4_VEIPT     - -MTQYTHIRNATGKLTIKNTTFLIDPFLAPKDTYPGFEGTFNYQQRMPMVDLPLSMDDLLSNVTAVVVTHTHLDHWDDTAINSIPKSLPIFVQNTADKELITSQGFIDVRIIFESLEFNGITLRKTGGSHGTVEMYANPVLAPLAGDAMGVIFEAADEPTVYLVGDTVWTSDVEKALLRFDPNVIIMNTGYAQILGFEDSIIMGTKDIGRMVVRKPEAKIIAVHMDTVNHTATSRKDVRKFIKGNNIESHVAVPEDGETITL 261
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------------Lactamase_B_2-3rpcD01 D:19-224                                                                                                                                                                                ------------------------------------- Pfam domains (1)
           Pfam domains (2) -------------------Lactamase_B_2-3rpcD02 D:19-224                                                                                                                                                                                ------------------------------------- Pfam domains (2)
           Pfam domains (3) -------------------Lactamase_B_2-3rpcD03 D:19-224                                                                                                                                                                                ------------------------------------- Pfam domains (3)
           Pfam domains (4) -------------------Lactamase_B_2-3rpcD04 D:19-224                                                                                                                                                                                ------------------------------------- Pfam domains (4)
         Sec.struct. author ...eeeeee..eeeeee..eeeee..............................hhhhhhh...eee....hhhhhhhhhhhhh.....eee.hhhhhhhhhhh....eee...eeee..eeeeee.....hhhhhh..hhhhhhh...eeeee......eeeee....hhhhhhhhhhhh..eeeee...............hhhhhhhhhhhh...eeeee..........hhhhhhhhhhhh.....ee......eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rpc D   0 AmTQYTHIRNATGKLTIKNTTFLIDPFLAPKDTYPGFEGTFNYQQRmPmVDLPLSmDDLLSNVTAVVVTHTHLDHWDDTAINSIPKSLPIFVQNTADKELITSQGFIDVRIIFESLEFNGITLRKTGGSHGTVEmYANPVLAPLAGDAmGVIFEAADEPTVYLVGDTVWTSDVEKALLRFDPNVIImNTGYAQILGFEDSIImGTKDIGRmVVRKPEAKIIAVHmDTVNHTATSRKDVRKFIKGNNIESHVAVPEDGETITL 261
                             |       9        19        29        39      | 49     |  59        69        79        89        99       109       119       129    |  139       149       159       169       179      |189       199  |    209|      219    |  229       239       249       259  
                             1-MSE                                       46-MSE   55-MSE                                                                        134-MSE       148-MSE                               186-MSE         202-MSE 210-MSE       224-MSE                                 
                                                                           48-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 3RPC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: Metallo-HOrase (67)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (D1BQT4_VEIPT | D1BQT4)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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 Related Entries

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