3GAS | pdb_00003gas

Crystal Structure of Helicobacter pylori Heme Oxygenase Hugz in Complex with Heme

PDB DOI: https://doi.org/10.2210/pdb3GAS/pdb

Classification: OXIDOREDUCTASE
Organism(s): Helicobacter pylori NCTC 11639
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-02-18 Released: 2010-02-23
Deposition Author(s): Jiang, F., Hu, Y.L., Guo, Y., Guo, G., Zou, Q.M., Wang, D.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.222 (Depositor), 0.215 (DCC)
R-Value Work:
0.192 (Depositor), 0.185 (DCC)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal Structure of Helicobacter pylori Heme Oxygenase Hugz in Complex with Heme

Jiang, F., Hu, Y.L., Guo, Y., Guo, G., Zou, Q.M., Wang, D.C.

To be published.

Macromolecule Content

Total Structure Weight: 184.5 kDa
Atom Count: 13,497
Modeled Residue Count: 1,484
Deposited Residue Count: 1,554
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, D, E A, B, C, D, E, F	259	Helicobacter pylori NCTC 11639	Mutation(s): 0 Gene Names: HugZ EC: 1.14.99.3 (PDB Primary Data), 1.14.99 (UniProt)
UniProt
Find proteins for O25087 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore O25087 Go to UniProtKB: O25087
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O25087
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain CA [auth E] SDF format, chain G [auth A] SDF format, chain GA [auth F] SDF format, chain L [auth B] SDF format, chain S [auth C] SDF format, chain X [auth D] MOL2 format, chain CA [auth E] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth F] MOL2 format, chain L [auth B] MOL2 format, chain S [auth C] MOL2 format, chain X [auth D] mmCIF format, chain CA [auth E] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth F] mmCIF format, chain L [auth B] mmCIF format, chain S [auth C] mmCIF format, chain X [auth D]	CA [auth E] G [auth A] GA [auth F] L [auth B] S [auth C] CA [auth E], G [auth A], GA [auth F], L [auth B], S [auth C], X [auth D]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain CA [auth E] Focus chain G [auth A] Focus chain GA [auth F] Focus chain L [auth B] Focus chain S [auth C] Focus chain X [auth D] Interactions & Density Focus chain CA [auth E] Focus chain G [auth A] Focus chain GA [auth F] Focus chain L [auth B] Focus chain S [auth C] Focus chain X [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain BA [auth D] SDF format, chain EA [auth E] SDF format, chain FA [auth E] SDF format, chain I [auth A] SDF format, chain IA [auth F] SDF format, chain J [auth A] SDF format, chain JA [auth F] SDF format, chain KA [auth F] SDF format, chain LA [auth F] SDF format, chain MA [auth F] SDF format, chain N [auth B] SDF format, chain NA [auth F] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain Z [auth D] SDF format, chain R [auth B] SDF format, chain K [auth A] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain EA [auth E] MOL2 format, chain FA [auth E] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth F] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth F] MOL2 format, chain KA [auth F] MOL2 format, chain LA [auth F] MOL2 format, chain MA [auth F] MOL2 format, chain N [auth B] MOL2 format, chain NA [auth F] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain Z [auth D] MOL2 format, chain R [auth B] MOL2 format, chain K [auth A] mmCIF format, chain AA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain EA [auth E] mmCIF format, chain FA [auth E] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth F] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth F] mmCIF format, chain KA [auth F] mmCIF format, chain LA [auth F] mmCIF format, chain MA [auth F] mmCIF format, chain N [auth B] mmCIF format, chain NA [auth F] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C] mmCIF format, chain Z [auth D] mmCIF format, chain R [auth B] mmCIF format, chain K [auth A]	AA [auth D] BA [auth D] EA [auth E] FA [auth E] I [auth A] AA [auth D], BA [auth D], EA [auth E], FA [auth E], I [auth A], IA [auth F], J [auth A], JA [auth F], K [auth A], KA [auth F], LA [auth F], MA [auth F], N [auth B], NA [auth F], O [auth B], P [auth B], Q [auth B], R [auth B], U [auth C], V [auth C], W [auth C], Z [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain EA [auth E] Focus chain FA [auth E] Focus chain I [auth A] Focus chain IA [auth F] Focus chain J [auth A] Focus chain JA [auth F] Focus chain K [auth A] Focus chain KA [auth F] Focus chain LA [auth F] Focus chain MA [auth F] Focus chain N [auth B] Focus chain NA [auth F] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain EA [auth E] Focus chain FA [auth E] Focus chain I [auth A] Focus chain IA [auth F] Focus chain J [auth A] Focus chain JA [auth F] Focus chain K [auth A] Focus chain KA [auth F] Focus chain LA [auth F] Focus chain MA [auth F] Focus chain N [auth B] Focus chain NA [auth F] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain Z [auth D]
AZI Query on AZI Download:Ideal Coordinates CCD File SDF format, chain HA [auth F] SDF format, chain T [auth C] SDF format, chain Y [auth D] SDF format, chain M [auth B] SDF format, chain H [auth A] SDF format, chain DA [auth E] MOL2 format, chain HA [auth F] MOL2 format, chain T [auth C] MOL2 format, chain Y [auth D] MOL2 format, chain M [auth B] MOL2 format, chain H [auth A] MOL2 format, chain DA [auth E] mmCIF format, chain HA [auth F] mmCIF format, chain T [auth C] mmCIF format, chain Y [auth D] mmCIF format, chain M [auth B] mmCIF format, chain H [auth A] mmCIF format, chain DA [auth E]	DA [auth E] H [auth A] HA [auth F] M [auth B] T [auth C] DA [auth E], H [auth A], HA [auth F], M [auth B], T [auth C], Y [auth D]	AZIDE ION N₃ IVRMZWNICZWHMI-UHFFFAOYSA-N		Interactions Focus chain DA [auth E] Focus chain H [auth A] Focus chain HA [auth F] Focus chain M [auth B] Focus chain T [auth C] Focus chain Y [auth D] Interactions & Density Focus chain DA [auth E] Focus chain H [auth A] Focus chain HA [auth F] Focus chain M [auth B] Focus chain T [auth C] Focus chain Y [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.222 (Depositor), 0.215 (DCC)
R-Value Work: 0.192 (Depositor), 0.185 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.33	α = 90
b = 139.34	β = 90
c = 152.9	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
SHARP	phasing
RESOLVE	phasing
CNS	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2010-02-23

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-02-23
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary