1V29 | pdb_00001v29

Crystal structure of Nitrile hydratase from a thermophile Bacillus smithii

• PDB DOI: https://doi.org/10.2210/pdb1V29/pdb

• Classification: LYASE
• Organism(s): Bacillus smithii
• Mutation(s): No 


• Deposited: 2003-10-09 Released: 2004-10-09 
• Deposition Author(s): Hourai, S., Miki, M., Takashima, Y., Mitsuda, S., Yanagi, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.226 (Depositor) 
• R-Value Work: 
  0.185 (Depositor) 
• R-Value Observed: 
  0.187 (Depositor) 

Literature

Crystal structure of nitrile hydratase from a thermophilic Bacillus smithii

Hourai, S., Miki, M., Takashima, Y., Mitsuda, S., Yanagi, K.

(2003) Biochem Biophys Res Commun 312: 340-345

• PubMed: 14637142 
• DOI: https://doi.org/10.1016/j.bbrc.2003.10.124
• Primary Citation Related Structures: 
  1V29


• PubMed Abstract: 
  

  The crystal structure of the nitrile hydratase (NHase) from Bacillus smithii SC-J05-1 was determined. Our analysis of the structure shows that some residues that seem to be responsible for substrate recognition are different from those of other NHases. In particular, the Phe52 in the beta subunit of NHase from B. smithii covers the metal center partially like a small lid and narrows the active site cleft. It is well known that the NHase from B. smithii especially prefers aliphatic nitriles for its substrate rather than aromatic ones, and we can now infer that the Phe52 residue may play a key role in the substrate specificity for this enzyme. This finding leads us to suggest that substitution of these residues may alter the substrate specificity of the enzyme.

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Organizational Affiliation: 
• Sumitomo Chemical Co, Ltd. Environmental Health Science Laboratory, 3-1-98 Kasugade-naka, Konohanaku, Osaka 554-8558, Japan. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 52.18 kDa 
• Atom Count: 3,648 
• Modeled Residue Count: 432 
• Deposited Residue Count: 449 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
nitrile hydratase a chain	A	220	Bacillus smithii	Mutation(s): 0  EC: 4.2.1.84
UniProt
Find proteins for Q84FS5 (Bacillus sp. RAPc8) Explore Q84FS5  Go to UniProtKB:  Q84FS5

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
nitrile hydratase b chain	B	229	Bacillus smithii	Mutation(s): 0  EC: 4.2.1.84

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CO	C [auth A]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.226 (Depositor) 
• R-Value Work:  0.185 (Depositor) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 158.42	α = 90
b = 158.42	β = 90
c = 126.77	γ = 90

Software Package:

Software Name	Purpose
crystal	data reduction
AMoRE	phasing
CNX	refinement
CrystalClear	data reduction
CrystalClear	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-10-09 
Deposition Author(s): Hourai, S., Miki, M., Takashima, Y., Mitsuda, S., Yanagi, K.

Revision History  

• Version 1.0: 2004-10-09
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description
• Version 1.4: 2023-12-27
  Changes: Data collection, Database references, Derived calculations