3VYH

Crystal structure of aW116R mutant of nitrile hydratase from Pseudonocardia thermophilla

• PDB DOI: https://doi.org/10.2210/pdb3VYH/pdb

• Classification: LYASE
• Organism(s): Pseudonocardia thermophila
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-09-25 Released: 2013-11-13 
• Deposition Author(s): Yamanaka, Y., Sato, M., Arakawa, T., Namima, S., Hori, S., Ohtaki, A., Noguchi, K., Katayama, Y., Yohda, M., Odaka, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free: 0.203 
• R-Value Work: 0.174 
• R-Value Observed: 0.175 

Literature

Effects of argnine residue around the substrate pocket on the substrate specificity of thiocyanate hydrolase

Yamanaka, Y., Sato, M., Arakawa, T., Namima, S., Hori, S., Ohtaki, A., Noguchi, K., Katayama, Y., Yohda, M., Odaka, M.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Macromolecule Content

• Total Structure Weight: 49.83 kDa 
• Atom Count: 3,818 
• Modelled Residue Count: 429 
• Deposited Residue Count: 437 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cobalt-containing nitrile hydratase subunit alpha	A	204	Pseudonocardia thermophila	Mutation(s): 1  EC: 4.2.1.84
UniProt
Find proteins for Q7SID2 (Pseudonocardia thermophila) Explore Q7SID2  Go to UniProtKB:  Q7SID2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cobalt-containing nitrile hydratase subunit beta	B	233	Pseudonocardia thermophila	Mutation(s): 0  EC: 4.2.1.84
UniProt
Find proteins for Q7SID3 (Pseudonocardia thermophila) Explore Q7SID3  Go to UniProtKB:  Q7SID3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CO	C [auth A]	COBALT (II) ION Co XLJKHNWPARRRJB-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: 1.63 Å
• R-Value Free: 0.203 
• R-Value Work: 0.174 
• R-Value Observed: 0.175 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.683	α = 90
b = 65.683	β = 90
c = 184.796	γ = 120

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: 2013-11-13 
Deposition Author(s): Yamanaka, Y., Sato, M., Arakawa, T., Namima, S., Hori, S., Ohtaki, A., Noguchi, K., Katayama, Y., Yohda, M., Odaka, M.

Revision History  

• Version 1.0: 2013-11-13
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2023-12-06
  Changes: Data collection