2D0Q | pdb_00002d0q

Complex of Fe-type NHase with Cyclohexyl isocyanide, photo-activated for 1hr at 277K

• PDB DOI: https://doi.org/10.2210/pdb2D0Q/pdb

• Classification: LYASE
• Organism(s): Rhodococcus erythropolis
• Mutation(s): Yes 


• Deposited: 2005-08-05 Released: 2006-02-05 
• Deposition Author(s): Nojiri, M., Kawano, Y., Hashimoto, K., Kamiya, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.165 (Depositor), 0.157 (DCC) 
• R-Value Work: 
  0.154 (Depositor), 0.158 (DCC) 
• R-Value Observed: 
  0.154 (Depositor) 

Literature

X-ray snap shots of Inhibitor Binding Process in Photo-reactive Nitrile Hydratase

Nojiri, M., Kawano, Y., Hashimoto, K., Kamiya, N.

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: 46.74 kDa 
• Atom Count: 3,833 
• Modeled Residue Count: 404 
• Deposited Residue Count: 418 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrile hydratase subunit alpha	A	206	Rhodococcus erythropolis	Mutation(s): 1  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): 0  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
CYI	H [auth A]	CYCLOHEXYL ISOCYANIDE C7 H11 N XYZMOVWWVXBHDP-UHFFFAOYSA-N
FE	C [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N
MG	D [auth A], E [auth A], F [auth A], G [auth A], I [auth B], J [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD	A	L-PEPTIDE LINKING	C3 H7 N O4 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.165 (Depositor), 0.157 (DCC) 
• R-Value Work:  0.154 (Depositor), 0.158 (DCC) 
• R-Value Observed: 0.154 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.352	α = 90
b = 60.201	β = 125.1
c = 81.585	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-02-05 
Deposition Author(s): Nojiri, M., Kawano, Y., Hashimoto, K., Kamiya, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2006-02-05
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary