4G3H | pdb_00004g3h

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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.230 (Depositor), 0.247 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.230 (Depositor) 

Literature

Structure and function studies on Helicobacter pylori arginase

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

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

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

Macromolecules

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 EC: 3.5.3.1
UniProt
Find proteins for O25949 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore O25949  Go to UniProtKB:  O25949

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN	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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.230 (Depositor), 0.247 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.230 (Depositor) 

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

Entry History 

Deposition Data

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

Revision History  

• 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