5K3B Hydrolase date May 19, 2016
title Crystal Structure Of The Fluoroacetate Dehalogenase Rpa1163 Asp110asnchloroacetate - Cocrystallized
authors P.Mehrabi, T.H.Kim, S.R.Prosser, E.F.Pai
compound source
Molecule: Fluoroacetate Dehalogenase
Chain: A, B
Ec: 3.8.1.3
Engineered: Yes
Mutation: Yes
Organism_scientific: Rhodopseudomonas Palustris (Strain Atc Cga009);
Organism_taxid: 258594
Strain: Atcc Baa-98 Cga009
Gene: Rpa1163
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1 21 1
R_factor 0.164 R_Free 0.196
crystal
cell
length a length b length c angle alpha angle beta angle gamma
41.837 78.956 84.986 90.00 103.28 90.00
method X-Ray Diffractionresolution 1.58 Å
ligand CL, R3W enzyme Hydrolase E.C.3.8.1.3 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceThe role of dimer asymmetry and protomer dynamics in enzyme catalysis., Kim TH, Mehrabi P, Ren Z, Sljoka A, Ing C, Bezginov A, Ye L, Pomes R, Prosser RS, Pai EF, Science. 2017 Jan 20;355(6322). pii: eaag2355. doi: 10.1126/science.aag2355. PMID:28104837
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (110 Kb) [Save to disk]
  • Biological Unit Coordinates (5k3b.pdb1.gz) 105 Kb
  • LPC: Ligand-Protein Contacts for 5K3B
  • CSU: Contacts of Structural Units for 5K3B
  • Structure Factors (1513 Kb)
  • Retrieve 5K3B in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5K3B from S2C, [Save to disk]
  • Re-refined 5k3b structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5K3B 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 5K3B
  • 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
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5k3b_B] [5k3b_A] [5k3b]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5K3B
  • Community annotation for 5K3B at PDBWiki (http://pdbwiki.org)

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