4FO5

Crystal structure of a thioredoxin-like protein (BDI_1100) from Parabacteroides distasonis ATCC 8503 at 2.02 A resolution

PDB DOI: https://doi.org/10.2210/pdb4FO5/pdb

Classification: OXIDOREDUCTASE
Organism(s): Parabacteroides distasonis ATCC 8503
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-06-20 Released: 2012-07-04
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.02 Å
R-Value Free: 0.208
R-Value Work: 0.176
R-Value Observed: 0.177

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of a thioredoxin-like protein (BDI_1100) from Parabacteroides distasonis ATCC 8503 at 2.02 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 16.19 kDa
Atom Count: 1,113
Modelled Residue Count: 136
Deposited Residue Count: 143
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
thioredoxin-like protein	A	143	Parabacteroides distasonis ATCC 8503	Mutation(s): 0 Gene Names: BDI_1100
UniProt
Find proteins for A6LAZ9 (Parabacteroides distasonis (strain ATCC 8503 / DSM 20701 / CIP 104284 / JCM 5825 / NCTC 11152)) Explore A6LAZ9 Go to UniProtKB: A6LAZ9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A6LAZ9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

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: 2.02 Å
R-Value Free: 0.208
R-Value Work: 0.176
R-Value Observed: 0.177
Space Group: P 1 2₁ 1
Diffraction Data: https://doi.org/10.18430/M34FO5

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.164	α = 90
b = 49.343	β = 112.18
c = 40.523	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SOLVE	phasing
XSCALE	data scaling
BUSTER-TNT	refinement
XDS	data reduction
BUSTER	refinement

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2012-07-04

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2012-07-04
Type: Initial release
Version 1.1: 2017-10-11
Changes: Data collection, Refinement description
Version 1.2: 2018-01-24
Changes: Database references
Version 1.3: 2023-02-01
Changes: Database references, Derived calculations

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 R01GM133198.