1JFC

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


Experimental Data Snapshot

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

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.,Sect.D 58: 81-89

  • Primary Citation of Related Structures:  

  • 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.Mol.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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
nitric-oxide reductase Cytochrome P450 55A1
A
404Fusarium oxysporumMutation(s): 0 
Gene Names: CYP55A1 (CYP55)
EC: 1.7.1.14
Find proteins for P23295 (Fusarium oxysporum)
Go to UniProtKB:  P23295
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

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

Download SDF File 
Download CCD File 
A
CARBON MONOXIDE
C O
UGFAIRIUMAVXCW-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free: 0.152 
  • R-Value Work: 0.117 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 54.866α = 90.00
b = 82.247β = 90.00
c = 85.798γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
MOSFLMdata reduction
CCP4data scaling
SHELXL-97refinement
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-12-20
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance