3ISH | pdb_00003ish

Crystal structure of Helicobacter pylori thioredoxin reductase

• PDB DOI: https://doi.org/10.2210/pdb3ISH/pdb

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


• Deposited: 2009-08-25 Released: 2009-10-06 
• Deposition Author(s): Sanders, D., Obiero, J., van Straaten, K.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.43 Å
• R-Value Free: 
  0.252 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Helicobacter pylori thioredoxin reductase

Sanders, D., Obiero, J., van Straaten, K.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 103.09 kDa 
• Atom Count: 7,715 
• Modeled Residue Count: 933 
• Deposited Residue Count: 933 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thioredoxin reductase	A, B, C	311	Helicobacter pylori 26695	Mutation(s): 0  Gene Names: HP0825 EC: 1.8.1.9
UniProt
Find proteins for P56431 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore P56431  Go to UniProtKB:  P56431

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	D [auth A], E [auth B], F [auth C]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.43 Å
• R-Value Free:  0.252 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.4	α = 90
b = 89.4	β = 90
c = 279.9	γ = 120

Software Package:

Software Name	Purpose
XDS	data scaling
MrBUMP	phasing
REFMAC	refinement
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-06 
Deposition Author(s): Sanders, D., Obiero, J., van Straaten, K.

Revision History  

• Version 1.0: 2009-10-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-27
  Changes: Structure summary