4GPH | pdb_00004gph

Structure of HmuO, heme oxygenase from Corynebacterium diphtheriae, in complex with the putative reaction intermediates between Fe3+-biliverdin and biliverdin (data set IV)

PDB DOI: https://doi.org/10.2210/pdb4GPH/pdb

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

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.205 (Depositor), 0.212 (DCC)
R-Value Work:
0.165 (Depositor), 0.172 (DCC)
R-Value Observed:
0.169 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 75.31 kDa
Atom Count: 5,733
Modeled Residue Count: 630
Deposited Residue Count: 645
Unique protein chains: 1

Macromolecules

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| 3D Structure

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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BLA Query on BLA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain N [auth C] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain N [auth C] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain N [auth C]	E [auth A], G [auth B], N [auth C]	BILIVERDINE IX ALPHA C₃₃ H₃₄ N₄ O₆ GWZYPXHJIZCRAJ-SRVCBVSDSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain N [auth C] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain N [auth C]
ASC Query on ASC Download:Ideal Coordinates CCD File SDF format, chain O [auth C] MOL2 format, chain O [auth C] mmCIF format, chain O [auth C]	O [auth C]	ASCORBIC ACID C₆ H₈ O₆ CIWBSHSKHKDKBQ-JLAZNSOCSA-N		Interactions Focus chain O [auth C] Interactions & Density Focus chain O [auth C]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] 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 P [auth C] SDF format, chain Q [auth C] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] 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 P [auth C] MOL2 format, chain Q [auth C] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] 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 P [auth C] mmCIF format, chain Q [auth C]	F [auth A] H [auth B] I [auth B] J [auth B] K [auth B] F [auth A], H [auth B], I [auth B], J [auth B], K [auth B], L [auth B], P [auth C], Q [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain P [auth C] Focus chain Q [auth C] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain P [auth C] Focus chain Q [auth C]
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain M [auth C] MOL2 format, chain D [auth A] MOL2 format, chain M [auth C] mmCIF format, chain D [auth A] mmCIF format, chain M [auth C]	D [auth A], M [auth C]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain M [auth C] Interactions & Density Focus chain D [auth A] Focus chain M [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.205 (Depositor), 0.212 (DCC)
R-Value Work: 0.165 (Depositor), 0.172 (DCC)
R-Value Observed: 0.169 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.065	α = 90
b = 62.966	β = 100.78
c = 107.728	γ = 90

Software Package:

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

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):

Unno, M.

Ikeda-Saito, M.

Revision History (Full details and data files)

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

4GPH | pdb_00004gph

Structure of HmuO, heme oxygenase from Corynebacterium diphtheriae, in complex with the putative reaction intermediates between Fe3+-biliverdin and biliverdin (data set IV)

Literature

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

Biological Assembly 1

Biological Assembly 2

Biological Assembly 3

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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