3LVZ Hydrolase date Feb 23, 2010
title New Refinement Of The Crystal Structure Of Bjp-1, A Subclass Metallo-Beta-Lactamase Of Bradyrhizobium Japonicum
authors J.D.Docquier, M.Benvenuti, V.Calderone, M.Stoczko, G.M.Rossolini S.Mangani
compound source
Molecule: Blr6230 Protein
Chain: A, B
Synonym: Subclass B3 Metallo-Beta-Lactamase
Engineered: Yes
Organism_scientific: Bradyrhizobium Japonicum
Organism_taxid: 224911
Strain: Usda 100
Gene: Blr6230, Bradyrhizobium
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Dh5
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-9a
symmetry Space Group: P 1
R_factor 0.162 R_Free 0.193
crystal
cell
length a length b length c angle alpha angle beta angle gamma
42.501 44.773 76.966 78.92 89.51 61.91
method X-Ray Diffractionresolution 1.40 Å
ligand ZN enzyme
Primary referenceHigh-resolution crystal structure of the subclass B3 metallo-beta-lactamase BJP-1: rational basis for substrate specificity and interaction with sulfonamides., Docquier JD, Benvenuti M, Calderone V, Stoczko M, Menciassi N, Rossolini GM, Mangani S, Antimicrob Agents Chemother. 2010 Oct;54(10):4343-51. Epub 2010 Aug 9. PMID:20696874
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (100 Kb) [Save to disk]
  • Biological Unit Coordinates (3lvz.pdb1.gz) 48 Kb
  • Biological Unit Coordinates (3lvz.pdb2.gz) 48 Kb
  • LPC: Ligand-Protein Contacts for 3LVZ
  • CSU: Contacts of Structural Units for 3LVZ
  • Structure Factors (1237 Kb)
  • Retrieve 3LVZ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3LVZ from S2C, [Save to disk]
  • Re-refined 3lvz structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3LVZ in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 3LVZ
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 3LVZ, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3lvz_A] [3lvz] [3lvz_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3LVZ: [Lactamase_B ] by SMART
  • Other resources with information on 3LVZ
  • Community annotation for 3LVZ at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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