4KND | pdb_00004knd

Thioredoxin from Anaeromyxobacter dehalogenans.

PDB DOI: https://doi.org/10.2210/pdb4KND/pdb

Classification: OXIDOREDUCTASE
Organism(s): Anaeromyxobacter dehalogenans 2CP-C
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-05-09 Released: 2013-05-22
Deposition Author(s): Osipiuk, J., Hatzos-Skintges, C., Clancy, S., Adkins, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG), Program for the Characterization of Secreted Effector Proteins (PCSEP)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.217 (Depositor), 0.247 (DCC)
R-Value Work:
0.183 (Depositor)
R-Value Observed:
0.185 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4KND

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

Literature

Thioredoxin from Anaeromyxobacter dehalogenans.

Osipiuk, J., Hatzos-skintges, C., Clancy, S., Adkins, J., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 24.53 kDa
Atom Count: 1,697
Modeled Residue Count: 209
Deposited Residue Count: 224
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thioredoxin	A, B	112	Anaeromyxobacter dehalogenans 2CP-C	Mutation(s): 0 Gene Names: Adeh_2496
UniProt
Find proteins for Q2IKT5 (Anaeromyxobacter dehalogenans (strain 2CP-C)) Explore Q2IKT5 Go to UniProtKB: Q2IKT5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2IKT5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	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: 0.217 (Depositor), 0.247 (DCC)
R-Value Work: 0.183 (Depositor)
R-Value Observed: 0.185 (Depositor)

Diffraction Data:

Space Group: I 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.731	α = 90
b = 76.954	β = 90
c = 77.208	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
SHELXCD	phasing
SHELXD	phasing
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing
HKL-3000	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2013-05-22

Deposition Author(s):

Hatzos-Skintges, C.

Midwest Center for Structural Genomics (MCSG)

Program for the Characterization of Secreted Effector Proteins (PCSEP)

Revision History (Full details and data files)

Version 1.0: 2013-05-22
Type: Initial release
Version 1.1: 2014-05-07
Changes: Structure summary
Version 1.2: 2017-11-15
Changes: Refinement description
Version 1.3: 2024-11-20
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.