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), 0.249 (DCC)
R-Value Work:
0.178 (Depositor), 0.181 (DCC)
R-Value Observed:
0.181 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Crystal structure of Helicobacter pylori thioredoxin reductase

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

To be published.

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

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P56431
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth B] SDF format, chain F [auth C] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B] MOL2 format, chain F [auth C] mmCIF format, chain D [auth A] mmCIF format, chain E [auth B] mmCIF format, chain F [auth C]	D [auth A], E [auth B], F [auth C]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.43 Å
R-Value Free: 0.252 (Depositor), 0.249 (DCC)
R-Value Work: 0.178 (Depositor), 0.181 (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

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2009-10-06

Deposition Author(s):

van Straaten, K.

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.