7JYP | pdb_00007jyp

Structure of thioredoxin reductase from the thermophilic eubacterium Thermosipho africanus TCF52B

PDB DOI: https://doi.org/10.2210/pdb7JYP/pdb

Classification: OXIDOREDUCTASE
Organism(s): Thermosipho africanus TCF52B
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-08-31 Released: 2021-10-06
Deposition Author(s): Sahtout, N., Kuttiyatveetil, J.R.A., Sanders, D.A.R.
Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.245 (Depositor), 0.240 (DCC)
R-Value Work:
0.214 (Depositor), 0.220 (DCC)
R-Value Observed:
0.216 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structure of thioredoxin reductase from the thermophilic eubacterium Thermosipho africanus TCF52B.

Sahtout, N., Kuttiyatveetil, J.R.A., Sanders, D.A.R.

To be published.

Macromolecule Content

Total Structure Weight: 38.89 kDa
Atom Count: 2,472
Modeled Residue Count: 305
Deposited Residue Count: 343
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thioredoxin reductase	A	343	Thermosipho africanus TCF52B	Mutation(s): 0 Gene Names: trxB, THA_1385 EC: 1.8.1.9
UniProt
Find proteins for B7ICV3 (Thermosipho africanus (strain TCF52B)) Explore B7ICV3 Go to UniProtKB: B7ICV3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B7ICV3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.245 (Depositor), 0.240 (DCC)
R-Value Work: 0.214 (Depositor), 0.220 (DCC)
R-Value Observed: 0.216 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.15	α = 90
b = 58.15	β = 90
c = 163.13	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALA	data scaling
AutoSol	phasing
Coot	model building

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2021-10-06

Deposition Author(s):

Kuttiyatveetil, J.R.A.

Sanders, D.A.R.

Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	--

Revision History (Full details and data files)

Version 1.0: 2021-10-06
Type: Initial release
Version 1.1: 2024-11-13
Changes: Data collection, Structure summary

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.