3B12 Hydrolase date Jun 19, 2011
title Crystal Structure Of The Fluoroacetate Dehalogenase D104 Mut Burkholderia Sp. Fa1 In Complex With Fluoroacetate
authors R.Omi, K.Hirotsu
compound source
Molecule: Fluoroacetate Dehalogenase
Chain: A, B
Ec: 3.8.1.3
Engineered: Yes
Mutation: Yes
Organism_scientific: Burkholderia Sp.
Organism_taxid: 36773
Strain: Fa1
Gene: Fac-Dex
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet21a
symmetry Space Group: P 21 21 21
R_factor 0.176 R_Free 0.185
crystal
cell
length a length b length c angle alpha angle beta angle gamma
53.497 85.065 136.354 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.20 Å
ligand FAH, MG enzyme Hydrolase E.C.3.8.1.3 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceSubstrate Specificity of Fluoroacetate Dehalogenase: An Insight from Crystallographic Analysis, Fluorescence Spectroscopy, and Theoretical Computations., Nakayama T, Kamachi T, Jitsumori K, Omi R, Hirotsu K, Esaki N, Kurihara T, Yoshizawa K, Chemistry. 2012 Jun 1. doi: 10.1002/chem.201103369. PMID:22674735
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (107 Kb) [Save to disk]
  • Biological Unit Coordinates (3b12.pdb1.gz) 102 Kb
  • LPC: Ligand-Protein Contacts for 3B12
  • CSU: Contacts of Structural Units for 3B12
  • Structure Factors (2667 Kb)
  • Retrieve 3B12 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3B12 from S2C, [Save to disk]
  • Re-refined 3b12 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3B12 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 3B12
  • 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 3B12, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3b12_A] [3b12_B] [3b12]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3B12
  • Community annotation for 3B12 at PDBWiki (http://pdbwiki.org)
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