3GNJ | pdb_00003gnj

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 (Depositor), 0.270 (DCC)
R-Value Work:
0.196 (Depositor), 0.203 (DCC)
R-Value Observed:
0.199 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3GNJ

This is version 1.2 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
Modeled Residue Count: 440
Deposited Residue Count: 444
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 (Depositor), 0.270 (DCC)
R-Value Work: 0.196 (Depositor), 0.203 (DCC)
R-Value Observed: 0.199 (Depositor)

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

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View more in-depth experimental data

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
Version 1.2: 2024-10-30
Changes: Data collection, Database references, Derived calculations, 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.