4GPF

Structure of the Fe3+-biliverdin-HmuO, heme oxygenase from Corynebacterium diphtheriae (data set III)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.190 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Crystal Structure 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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Heme oxygenase
A, B, C
215Corynebacterium diphtheriaeMutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ54AI1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BLA
Query on BLA

Download Ideal Coordinates CCD File 
D [auth A],
N [auth B],
S [auth C]
BILIVERDINE IX ALPHA
C33 H34 N4 O6
GWZYPXHJIZCRAJ-SRVCBVSDSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
I [auth B]
J [auth B]
F [auth A],
G [auth A],
H [auth A],
I [auth B],
J [auth B],
K [auth B],
L [auth B],
M [auth B],
O [auth C],
P [auth C],
Q [auth C],
R [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
FE
Query on FE

Download Ideal Coordinates CCD File 
E [auth A]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.190 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.937α = 90
b = 62.539β = 101.09
c = 107.589γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
CNSrefinement
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-08-21
    Type: Initial release
  • Version 1.1: 2024-03-20
    Changes: Data collection, Database references, Derived calculations