1ROM | pdb_00001rom

CRYSTAL STRUCTURE OF NITRIC REDUCTASE FROM DENITRIFYING FUNGUS FUSARIUM OXYSPORUM

• PDB DOI: https://doi.org/10.2210/pdb1ROM/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Fusarium oxysporum
• Mutation(s): No 


• Deposited: 1997-03-24 Released: 1997-10-15 
• Deposition Author(s): Park, S.-Y., Nakagawa, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.266 (Depositor) 
• R-Value Work: 
  0.197 (Depositor) 
• R-Value Observed: 
  0.197 (Depositor) 

Literature

Crystal structure of nitric oxide reductase from denitrifying fungus Fusarium oxysporum.

Park, S.Y., Shimizu, H., Adachi, S., Nakagawa, A., Tanaka, I., Nakahara, K., Shoun, H., Obayashi, E., Nakamura, H., Iizuka, T., Shiro, Y.

(1997) Nat Struct Biol 4: 827-832

• PubMed: 9334748 
• DOI: https://doi.org/10.1038/nsb1097-827
• Primary Citation Related Structures: 
  1ROM, 2ROM


• PubMed Abstract: 
  

  Structures of nitric oxide reductase (NOR) in the ferric resting and the ferrous CO states have been solved at 2.0 A resolution. These structures provide significant new insights into how NO is reduced in biological systems. The haem distal pocket is open to solvent, implicating this region as a possible NADH binding site. In combination with mutagenesis results, a hydrogen-bonding network from the water molecule adjacent to the iron ligand to the protein surface of the distal pocket through the hydroxyl group of Ser 286 and the carboxyl group of Asp 393 can be assigned to a pathway for proton delivery during the NO reduction reaction.

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Organizational Affiliation: 
• Institute of Physical and Chemical Research (RIKEN), Saitama, Japan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 45.04 kDa 
• Atom Count: 3,301 
• Modeled Residue Count: 399 
• Deposited Residue Count: 403 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CYTOCHROME P450	A	403	Fusarium oxysporum	Mutation(s): 0  EC: 1.14 (PDB Primary Data), 1.7.1.14 (UniProt)
UniProt
Find proteins for P23295 (Fusarium oxysporum) Explore P23295  Go to UniProtKB:  P23295

Small Molecules

Ligands 1 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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.266 (Depositor) 
• R-Value Work:  0.197 (Depositor) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.99	α = 90
b = 82.66	β = 90
c = 87.21	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
CCP4	data scaling
Agrovata	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-10-15 
Deposition Author(s): Park, S.-Y., Nakagawa, A.

Revision History  

• Version 1.0: 1997-10-15
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description