3GNJ

The crystal structure of a thioredoxin-related protein from Desulfitobacterium hafniense DCB

PDB DOI: https://doi.org/10.2210/pdb3GNJ/pdb

Classification: structural genomics, unknown function
Organism(s): Desulfitobacterium hafniense DCB-2
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-03-17 Released: 2009-05-12
Deposition Author(s): Tan, K., Volkart, L., Gu, M., Kinney, J.N., Babnigg, G., Kerfeld, C., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free: 0.266
R-Value Work: 0.196
R-Value Observed: 0.199

wwPDB Validation 3D Report Full Report

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

Literature

The crystal structure of a thioredoxin-related protein from Desulfitobacterium hafniense DCB

Tan, K., Volkart, L., Gu, M., Kinney, J.N., Babnigg, G., Kerfeld, C., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 52.51 kDa
Atom Count: 3,728
Modelled Residue Count: 440
Deposited Residue Count: 444
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 domain protein	A, B, C, D	111	Desulfitobacterium hafniense DCB-2	Mutation(s): 0 Gene Names: Desulfitobacterium hafniense, Dhaf_4889
UniProt
Find proteins for B8G0E7 (Desulfitobacterium hafniense (strain DSM 10664 / DCB-2)) Explore B8G0E7 Go to UniProtKB: B8G0E7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B8G0E7
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free: 0.266
R-Value Work: 0.196
R-Value Observed: 0.199
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.167	α = 90
b = 66.341	β = 105.67
c = 70.163	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
DM	model building
ARP	model building
WARP	model building
HKL-3000	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2009-05-12

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2009-05-12
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance

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.