4G3H

Crystal structure of helicobacter pylori arginase

PDB DOI: https://doi.org/10.2210/pdb4G3H/pdb

Classification: HYDROLASE
Organism(s): Helicobacter pylori 26695
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-07-13 Released: 2012-08-01
Deposition Author(s): Zhang, J., Zhang, X., Li, D., Hu, Y., Zou, Q., Wang, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.230
R-Value Work: 0.218
R-Value Observed: 0.230

wwPDB Validation 3D Report Full Report

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

Literature

Structure and function studies on Helicobacter pylori arginase

Zhang, J., Zhang, X., Li, D., Hu, Y., Zou, Q., Wang, D.

To be published.

Macromolecule Content

Total Structure Weight: 152.65 kDa
Atom Count: 10,439
Modelled Residue Count: 1,216
Deposited Residue Count: 1,320
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Arginase (RocF)	A, B, C, D	330	Helicobacter pylori 26695	Mutation(s): 0 Gene Names: HP_1399
UniProt
Find proteins for O25949 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore O25949 Go to UniProtKB: O25949
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O25949
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain I [auth C] SDF format, chain J [auth C] SDF format, chain K [auth D] SDF format, chain L [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth C] MOL2 format, chain J [auth C] MOL2 format, chain K [auth D] MOL2 format, chain L [auth D]	E [auth A] F [auth A] G [auth B] H [auth B] I [auth C] E [auth A], F [auth A], G [auth B], H [auth B], I [auth C], J [auth C], K [auth D], L [auth D]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth D] Focus chain L [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth D] Focus chain L [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.230
R-Value Work: 0.218
R-Value Observed: 0.230
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.69	α = 90
b = 102.24	β = 90
c = 148.61	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASES	phasing
CNS	refinement
DENZO	data reduction
SCALA	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-08-01

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-08-01
Type: Initial release
Version 1.1: 2014-12-17
Changes: Data collection
Version 1.2: 2024-03-20
Changes: Data collection, Database references, Derived calculations

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Help and Resources

4G3H

Crystal structure of helicobacter pylori arginase

Structure and function studies on Helicobacter pylori arginase

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)