3X28 | pdb_00003x28

Crystal structure of Nitrile Hydratase mutant bR56K

• PDB DOI: https://doi.org/10.2210/pdb3X28/pdb

• Classification: LYASE
• Organism(s): Rhodococcus erythropolis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2014-12-12 Released: 2015-12-23 
• Deposition Author(s): Yamanaka, Y., Hashimoto, K., Noguchi, K., Yohda, M., Odaka, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.218 (Depositor), 0.226 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 46.67 kDa 
• Atom Count: 3,459 
• Modeled Residue Count: 409 
• Deposited Residue Count: 419 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrile hydratase subunit alpha	A	207	Rhodococcus erythropolis	Mutation(s): 0  Gene Names: nthA EC: 4.2.1.84
UniProt
Find proteins for P13448 (Rhodococcus erythropolis) Explore P13448  Go to UniProtKB:  P13448

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrile hydratase subunit beta	B	212	Rhodococcus erythropolis	Mutation(s): 1  Gene Names: nthB, nha2 EC: 4.2.1.84
UniProt
Find proteins for P13449 (Rhodococcus erythropolis) Explore P13449  Go to UniProtKB:  P13449

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FE	C [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N
CL	E [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	D [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD	A	L-PEPTIDE LINKING	C3 H7 N O4 S		CYS
CSO	A	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.218 (Depositor), 0.226 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.786	α = 90
b = 60.579	β = 124.97
c = 81.996	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-12-23 
Deposition Author(s): Yamanaka, Y., Hashimoto, K., Noguchi, K., Yohda, M., Odaka, M.

Revision History  

• Version 1.0: 2015-12-23
  Type: Initial release
  
• Version 1.1: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary