2A9E

Helicobacter pylori catalase compound I

PDB DOI: https://doi.org/10.2210/pdb2A9E/pdb

Classification: OXIDOREDUCTASE
Organism(s): Helicobacter pylori
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2005-07-11 Released: 2006-06-20
Deposition Author(s): Loewen, P.C., Carpena, X., Fita, I.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free: 0.178
R-Value Work: 0.137
R-Value Observed: 0.139

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Helicobacter pylori catalase compound I

Loewen, P.C., Carpena, X., Fita, I.

To be published.

Macromolecule Content

Total Structure Weight: 118.91 kDa
Atom Count: 9,112
Modelled Residue Count: 982
Deposited Residue Count: 1,010
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
KatA Catalase	A, B	505	Helicobacter pylori	Mutation(s): 4 Gene Names: katA EC: 1.11.1.6
UniProt
Find proteins for P77872 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore P77872 Go to UniProtKB: P77872
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P77872
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 D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B]	D [auth A], F [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
O Query on O Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B]	E [auth A], G [auth B]	OXYGEN ATOM O XLYOFNOQVPJJNP-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Interactions & Density Focus chain E [auth A] Focus chain G [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MHO Query on MHO	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₃ S		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free: 0.178
R-Value Work: 0.137
R-Value Observed: 0.139
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.385	α = 90
b = 154.286	β = 90
c = 95.808	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2006-06-20

Deposition Author(s):

Loewen, P.C.

Carpena, X.

Fita, I.

Revision History (Full details and data files)

Version 1.0: 2006-06-20
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Derived calculations, Refinement description, Version format compliance
Version 1.3: 2023-08-23
Changes: Data collection, Database references, Derived calculations, Refinement description

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2A9E

Helicobacter pylori catalase compound I

Helicobacter pylori catalase compound I

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)