4GPC

Structure of the biliverdin-HmuO, heme oxygenase from Corynebacterium diphtheriae

• PDB DOI: https://doi.org/10.2210/pdb4GPC/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Corynebacterium diphtheriae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-08-20 Released: 2013-08-21 
• Deposition Author(s): Unno, M., Ikeda-Saito, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.203 
• R-Value Work: 0.168 
• R-Value Observed: 0.170 

Literature

Crystal Structures of the Substrate-Free and the Product-Bound forms of HmuO, a Heme Oxygenase from Corynebacterium diphtheriae

Unno, M., Ardevol, A., Rovira, C., Ikeda-Saito, M.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 75.01 kDa 
• Atom Count: 5,633 
• Modelled Residue Count: 631 
• Deposited Residue Count: 645 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heme oxygenase	A, B, C	215	Corynebacterium diphtheriae	Mutation(s): 0  EC: 1.14.99.3 (PDB Primary Data), 1.14.14.18 (UniProt)
UniProt
Find proteins for Q54AI1 (Corynebacterium diphtheriae) Explore Q54AI1  Go to UniProtKB:  Q54AI1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BLA	D [auth A], G [auth B], K [auth C]	BILIVERDINE IX ALPHA C33 H34 N4 O6 GWZYPXHJIZCRAJ-SRVCBVSDSA-N
ASC	L [auth C]	ASCORBIC ACID C6 H8 O6 CIWBSHSKHKDKBQ-JLAZNSOCSA-N
SO4	E [auth A], F [auth A], H [auth B], I [auth B], J [auth B], M [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.203 
• R-Value Work: 0.168 
• R-Value Observed: 0.170 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.114	α = 90
b = 63.091	β = 100.73
c = 107.558	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
CNS	refinement
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-08-21 
Deposition Author(s): Unno, M., Ikeda-Saito, M.

Revision History  

• Version 1.0: 2013-08-21
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references, Structure summary