3X28

Crystal structure of Nitrile Hydratase mutant bR56K


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Reaction intermediate of nitrile hydratase determined by time-resolved crystallography reveals the cysteine-sulfenic acid ligand to be a catalytic nucleophile

Yamanaka, Y.Hashimoto, K.Noguchi, K.Yohda, M.Odaka, M.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nitrile hydratase subunit alpha
A
207Rhodococcus erythropolisMutation(s): 0 
Gene Names: nthA
EC: 4.2.1.84
Find proteins for P13448 (Rhodococcus erythropolis)
Go to UniProtKB:  P13448
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nitrile hydratase subunit beta
B
212Rhodococcus erythropolisMutation(s): 1 
Gene Names: nthB (nha2)
EC: 4.2.1.84
Find proteins for P13449 (Rhodococcus erythropolis)
Go to UniProtKB:  P13449
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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Download CCD File 
B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

Download SDF File 
Download CCD File 
A
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
A
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
CSD
Query on CSD
A
L-PEPTIDE LINKINGC3 H7 N O4 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.180 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 114.786α = 90.00
b = 60.579β = 124.97
c = 81.996γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data collection
HKL-2000data reduction
REFMACrefinement
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-12-23
    Type: Initial release