1JFC | pdb_00001jfc

X-ray structure of nitric oxide reductase (cytochrome P450nor) in the ferrous CO state at atomic resolution

• PDB DOI: https://doi.org/10.2210/pdb1JFC/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Fusarium oxysporum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2001-06-20 Released: 2001-12-20 
• Deposition Author(s): Shimizu, H., Adachi, S., Park, S.Y., Shiro, Y., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.05 Å
• R-Value Free: 
  0.152 (Depositor) 
• R-Value Work: 
  0.117 (Depositor) 

Literature

X-ray structure of nitric oxide reductase (cytochrome P450nor) at atomic resolution.

Shimizu, H., Park, S.Y., Shiro, Y., Adachi, S.

(2002) Acta Crystallogr D Biol Crystallogr 58: 81-89

• PubMed: 11752781 
• DOI: https://doi.org/10.1107/s0907444901017383
• Primary Citation Related Structures: 
  1JFB, 1JFC


• PubMed Abstract: 
  

  Crystal structures of the nitric oxide reductase cytochrome P450nor (P450nor) in the ferric resting and the ferrous carbonmonoxy (CO) states have been determined at 1.00 and 1.05 A resolution, respectively. P450nor consists of 403 amino-acid residues (46 kDa) and is one of the largest proteins refined to this resolution so far. The final models have conventional R factors of 10.2% (ferric resting) and 11.7% (ferrous CO), with mean coordinate errors of 0.028 (ferric resting) and 0.030 A (ferrous CO) as calculated from inversion of the full positional least-squares matrix. Owing to the atomic resolution, novel features are found in the refined structures. Firstly, two orientations of the haem are observed both in the ferric resting and the ferrous CO states. Secondly, a disordered water molecule bound to the haem iron is found in the ferric resting state. In addition, the accurate structures at atomic resolution enabled the examination of general stereochemical parameters that are commonly used in refinement cycles of protein structures.

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Organizational Affiliation: 
• RIKEN Harima Institute/SPring-8, 1-1-1 Kouto, Mikazuki, Sayo, Hyogo 679-5148, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 45.26 kDa 
• Atom Count: 4,296 
• Modeled Residue Count: 399 
• Deposited Residue Count: 404 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
nitric-oxide reductase Cytochrome P450 55A1	A	404	Fusarium oxysporum	Mutation(s): 0  EC: 1.7.99.7 (PDB Primary Data), 1.7.1.14 (UniProt)
UniProt
Find proteins for P23295 (Fusarium oxysporum) Explore P23295  Go to UniProtKB:  P23295

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CMO	C [auth A]	CARBON MONOXIDE C O UGFAIRIUMAVXCW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.05 Å
• R-Value Free:  0.152 (Depositor) 
• R-Value Work:  0.117 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.866	α = 90
b = 82.247	β = 90
c = 85.798	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
SHELXL-97	refinement
MOSFLM	data reduction
CCP4	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-12-20 
Deposition Author(s): Shimizu, H., Adachi, S., Park, S.Y., Shiro, Y., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2001-12-20
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references, Derived calculations