3DML

Crystal structure of the periplasmic thioredoxin SoxS from Paracoccus pantotrophus (reduced form)

PDB DOI: https://doi.org/10.2210/pdb3DML/pdb

Classification: OXIDOREDUCTASE
Organism(s): Paracoccus denitrificans
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-07-01 Released: 2008-08-26
Deposition Author(s): Carius, Y., Friedrich, C.G., Scheidig, A.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.201
R-Value Work: 0.154
R-Value Observed: 0.157

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of the periplasmic thioredoxin SoxS from Paracoccus pantotrophus indicates a dual Trx/Grx functionality for activation of chemotrophic sulfur oxidation in vivo

Carius, Y., Rother, D., Friedrich, C.G., Scheidig, A.J.

To be published.

Macromolecule Content

Total Structure Weight: 13.32 kDa
Atom Count: 961
Modelled Residue Count: 96
Deposited Residue Count: 116
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein	A	116	Paracoccus denitrificans	Mutation(s): 0 Gene Names: soxS EC: 1.8.4
UniProt
Find proteins for Q8KM22 (Paracoccus denitrificans) Explore Q8KM22 Go to UniProtKB: Q8KM22
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8KM22
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.201
R-Value Work: 0.154
R-Value Observed: 0.157
Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.909	α = 90
b = 80.909	β = 90
c = 33.212	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
DENZO	data reduction
SCALEPACK	data scaling
Auto-Rickshaw	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2008-08-26

Deposition Author(s):

Friedrich, C.G.

Revision History (Full details and data files)

Version 1.0: 2008-08-26
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.