1JFB

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.00 Å
  • R-Value Free: 0.139 
  • R-Value Work: 0.102 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


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

  • DOI: 10.1107/s0907444901017383
  • Primary Citation of Related Structures:  
    1JFC, 1JFB

  • 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 ...

    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.


    Related Citations: 
    • 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
    • Proton Delivery in No Reduction by Fungal Nitric-Oxide Reductase. Cryogenic Crystallography, Spectroscopy, and Kinetics of Ferric-No Complexes of Wild- Type and Mutant Enzymes
      Shimizu, H., Obayashi, E., Gomi, Y., Arakawa, H., Park, S.Y., Nakamura, H., Adachi, S., Shoun, H., Shiro, Y.
      (2000) J Biol Chem 275: 4816

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
nitric-oxide reductase cytochrome P450 55A1A404Fusarium oxysporumMutation(s): 0 
Gene Names: CYP55A1CYP55
EC: 1.7.99.7 (PDB Primary Data), 1.7.1.14 (UniProt)
Find proteins for P23295 (Fusarium oxysporum)
Explore P23295 
Go to UniProtKB:  P23295
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.00 Å
  • R-Value Free: 0.139 
  • R-Value Work: 0.102 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.661α = 90
b = 82.132β = 90
c = 85.843γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
SHELXL-97refinement
MOSFLMdata reduction
CCP4data scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

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