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(-) Description

Title :  CRYSTAL STRUCTURE OF THE METALLO-BETA-LACTAMASE VIM-31 IN ITS OXIDIZED FORM AT 1.88 A
 
Authors :  K. Herzog, K. M. Hoffmann
Date :  27 Jun 12  (Deposition) - 26 Jun 13  (Release) - 01 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.88
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Metallo-Beta-Lactamase Superfamily, Beta-Lactam Hydrolyzing Enzyme, Zinc Binding, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. B. Kupper, K. Herzog, S. Bennink, P. Schlomer, P. Bogaerts, Y. Glupczynski, R. Fischer, C. Bebrone, K. M. Hoffmann
The Three-Dimensional Structure Of Vim-31 - A Metallo-Beta-Lactamase From Enterobacter Cloacae In Its Native And Oxidized Form.
Febs J. V. 282 2352 2015
PubMed-ID: 25825035  |  Reference-DOI: 10.1111/FEBS.13283

(-) Compounds

Molecule 1 - METALLO-BETA-LACTAMASE VIM-31
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET28A
    Fragment: UNP RESIDUES 31-266
    Gene: BLAVIM-31
    Mutation: YES
    Organism Scientific: ENTEROBACTER CLOACAE
    Organism Taxid: 550
    Strain: 11236

 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  (3, 10)

Asymmetric Unit (3, 10)
No.NameCountTypeFull Name
1CL4Ligand/IonCHLORIDE ION
2OCS2Mod. Amino AcidCYSTEINESULFONIC ACID
3ZN4Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2OCS1Mod. Amino AcidCYSTEINESULFONIC ACID
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2OCS1Mod. Amino AcidCYSTEINESULFONIC ACID
3ZN-1Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:112 , HIS A:114 , HIS A:177 , OCS A:196 , HOH A:413 , HOH A:450BINDING SITE FOR RESIDUE ZN A 301
2AC2SOFTWAREHIS A:151 , HIS A:249 , HOH A:640 , HOH A:641 , HOH A:642 , HOH A:643BINDING SITE FOR RESIDUE ZN A 302
3AC3SOFTWAREGLY A:155 , SER A:157 , HOH A:630BINDING SITE FOR RESIDUE CL A 303
4AC4SOFTWAREARG A:164 , GLY A:166BINDING SITE FOR RESIDUE CL A 304
5AC5SOFTWAREHIS B:151 , HIS B:249 , HOH B:620 , HOH B:623 , HOH B:624BINDING SITE FOR RESIDUE ZN B 301
6AC6SOFTWAREHIS B:112 , HIS B:114 , HIS B:177 , OCS B:196 , HOH B:407 , HOH B:448BINDING SITE FOR RESIDUE ZN B 302
7AC7SOFTWAREGLY B:155 , HOH B:614BINDING SITE FOR RESIDUE CL B 303
8AC8SOFTWAREGLY B:166 , HOH B:556BINDING SITE FOR RESIDUE CL B 304

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4FSB)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4FSB)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4FSB)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4FSB)

(-) Exons   (0, 0)

(no "Exon" information available for 4FSB)

(-) 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:232
                                                                                                                                                                                                                                                                        
               SCOP domains d4fsba_ A: automated matches                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeeee..eeeeeeeeee..eeeeeeeeeeee..eeeee....hhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhh..eeeehhhhhhhhhhhh.....ee........eeeee..eeeee..........eeee....eeeeehhh.................hhhhhhhhhhhhh....eeee.......hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fsb A  29 GEYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGcAIHELSRTSAGNVADADLAEWPTSIERIQQRYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNR 260
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258  
                                                                                                                                                                                                 196-OCS                                                            


Chain B from PDB  Type:PROTEIN  Length:232
                                                                                                                                                                                                                                                                        
               SCOP domains d4fsbb_ B: automated matches                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeeee..eeeeeeeeee..eeeeeeeeeeee..eeeee....hhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhh..eeeehhhhhhhhhhhh.....ee........eeeee..eeeee..........eee.....eeeeehhh.................hhhhhhhhhhhhh....eeee.......hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fsb B  29 GEYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGcAIHELSRTSAGNVADADLAEWPTSIERIQQRYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNR 260
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258  
                                                                                                                                                                                                 196-OCS
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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  (1, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4FSB)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4FSB)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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(-) Related Entries Specified in the PDB File

4fr7 CRYSTAL STRUCTURE OF THE METALLO-BETA-LACTAMASE VIM-31 IN ITS REDUCED FORM AT 1.61 A