3X20 Lyase date Dec 03, 2014
title Crystal Structure Of Nitrile Hydratase Mutant Br56k Complexe Trimethylacetonitrile, Photo-Activated For 25 Min
authors Y.Yamanaka, K.Hashimoto, N.Noguchi, M.Yohda, M.Odaka
compound source
Molecule: Nitrile Hydratase Subunit Alpha
Chain: A
Synonym: Nhase, Nitrilase
Ec: 4.2.1.84
Engineered: Yes
Organism_scientific: Rhodococcus Erythropolis
Organism_taxid: 1833
Gene: Ntha
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Nitrile Hydratase Subunit Beta
Chain: B
Synonym: Nhase, Nitrilase
Ec: 4.2.1.84
Engineered: Yes
Mutation: Yes

Organism_scientific: Rhodococcus Erythropolis
Organism_taxid: 1833
Gene: Nha2, Nthb
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: C 1 2 1
R_factor 0.142 R_Free 0.162
crystal
cell
length a length b length c angle alpha angle beta angle gamma
114.796 60.381 82.086 90.00 124.97 90.00
method X-Ray Diffractionresolution 1.18 Å
ligand CL, CSD, CSO, FE, MG, TAN enzyme Lyase E.C.4.2.1.84 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


B


Primary referenceTime-Resolved Crystallography of the Reaction Intermediate of Nitrile Hydratase: Revealing a Role for the Cysteinesulfenic Acid Ligand as a Catalytic Nucleophile., Yamanaka Y, Kato Y, Hashimoto K, Iida K, Nagasawa K, Nakayama H, Dohmae N, Noguchi K, Noguchi T, Yohda M, Odaka M, Angew Chem Int Ed Engl. 2015 Sep 7;54(37):10763-7. doi: 10.1002/anie.201502731. PMID:26333053
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (158 Kb) [Save to disk]
  • Biological Unit Coordinates (3x20.pdb1.gz) 153 Kb
  • LPC: Ligand-Protein Contacts for 3X20
  • CSU: Contacts of Structural Units for 3X20
  • Structure Factors (2745 Kb)
  • Retrieve 3X20 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3X20 from S2C, [Save to disk]
  • Re-refined 3x20 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3X20 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 3X20
  • 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: [3x20_A] [3x20_B] [3x20]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3X20
  • Community annotation for 3X20 at PDBWiki (http://pdbwiki.org)

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