4GPF | pdb_00004gpf

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

PDB DOI: https://doi.org/10.2210/pdb4GPF/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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.239 (Depositor), 0.250 (DCC)
R-Value Work:
0.185 (Depositor), 0.201 (DCC)
R-Value Observed:
0.190 (Depositor)

wwPDB Validation 3D Report Full Report

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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.

Macromolecule Content

Total Structure Weight: 75.47 kDa
Atom Count: 5,494
Modeled Residue Count: 624
Deposited Residue Count: 645
Unique protein chains: 1

Macromolecules

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q54AI1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BLA Query on BLA Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain N [auth B] SDF format, chain S [auth C] MOL2 format, chain D [auth A] MOL2 format, chain N [auth B] MOL2 format, chain S [auth C] mmCIF format, chain D [auth A] mmCIF format, chain N [auth B] mmCIF format, chain S [auth C]	D [auth A], N [auth B], S [auth C]	BILIVERDINE IX ALPHA C₃₃ H₃₄ N₄ O₆ GWZYPXHJIZCRAJ-SRVCBVSDSA-N		Interactions Focus chain D [auth A] Focus chain N [auth B] Focus chain S [auth C] Interactions & Density Focus chain D [auth A] Focus chain N [auth B] Focus chain S [auth C]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain R [auth C] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C]	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		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C]
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.239 (Depositor), 0.250 (DCC)
R-Value Work: 0.185 (Depositor), 0.201 (DCC)
R-Value Observed: 0.190 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.937	α = 90
b = 62.539	β = 101.09
c = 107.589	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-08-21

Deposition Author(s):

Ikeda-Saito, M.

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.