Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 31.23 kDa 
• Atom Count: 1845 
• Modelled Residue Count: 214 
• Deposited Residue Count: 267 
• Unique protein chains: 1

1DVE

CRYSTAL STRUCTURE OF RAT HEME OXYGENASE-1 IN COMPLEX WITH HEME

• PDB DOI: 10.2210/pdb1DVE/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2000-01-20 Released: 2000-04-12 
• Deposition Author(s): Sugishima, M., Omata, Y., Kakuta, Y., Sakamoto, H., Noguchi, M., Fukuyama, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.268 
• R-Value Work: 0.214 

Literature

Crystal structure of rat heme oxygenase-1 in complex with heme.

Sugishima, M., Omata, Y., Kakuta, Y., Sakamoto, H., Noguchi, M., Fukuyama, K.

(2000) FEBS Lett 471: 61-66

• PubMed: 10760513 
• DOI: 10.1016/s0014-5793(00)01353-3
• Primary Citation of Related Structures:  
  1DVE, 1DVG


• PubMed Abstract: 
  

Heme oxygenase catalyzes the oxidative cleavage of protoheme to biliverdin, the first step of heme metabolism utilizing O(2) and NADPH. We determined the crystal structures of rat heme oxygenase-1 (HO-1)-heme and selenomethionyl HO-1-heme complexes. Heme is sandwiched between two helices with the delta-meso edge of the heme being exposed to the surface. Gly143N forms a hydrogen bond to the distal ligand of heme, OH(-). The distance between Gly143N and the ligand is shorter than that in the human HO-1-heme complex. This difference may be related to a pH-dependent change of the distal ligand of heme. Flexibility of the distal helix may control the stability of the coordination of the distal ligand to heme iron. The possible role of Gly143 in the heme oxygenase reaction is discussed.

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Related Citations: 

• Crystallization and Preliminary X-ray Diffraction Studies on the Water Soluble Form of Rat Heme Oxygenase-1 in Complex with Heme
  Omata, Y., Asada, S., Sakamoto, H., Fukuyama, K., Noguchi, M.
  (1998) Acta Crystallogr D Biol Crystallogr 54: 1017

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Organizational Affiliation: 

Department of Biology, Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HEME OXYGENASE-1	A	267	Rattus norvegicus	Mutation(s): 0  Gene Names: Hmox1 EC: 1.14.99.3 (PDB Primary Data), 1.14.14.18 (UniProt)
UniProt
Find proteins for P06762 (Rattus norvegicus) Explore P06762  Go to UniProtKB:  P06762

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: 2.40 Å
• R-Value Free: 0.268 
• R-Value Work: 0.214 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.139	α = 90
b = 56.139	β = 90
c = 183.984	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2000-01-20 
• Released Date: 2000-04-12 
Deposition Author(s): Sugishima, M., Omata, Y., Kakuta, Y., Sakamoto, H., Noguchi, M., Fukuyama, K.

Revision History  

• Version 1.0: 2000-04-12
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance