3JU3 | pdb_00003ju3

Crystal structure of alpha chain of probable 2-oxoacid ferredoxin oxidoreductase from Thermoplasma acidophilum

PDB DOI: https://doi.org/10.2210/pdb3JU3/pdb

Classification: OXIDOREDUCTASE
Organism(s): Thermoplasma acidophilum
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2009-09-14 Released: 2009-09-22
Deposition Author(s): Chang, C., Marshall, N., Bearden, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.236 (Depositor), 0.271 (DCC)
R-Value Work:
0.198 (Depositor), 0.230 (DCC)
R-Value Observed:
0.200 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3JU3

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

Literature

Crystal structure of alpha chain of probable 2-oxoacid ferredoxin oxidoreductase from Thermoplasma acidophilum

Chang, C., Marshall, N., Bearden, J., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 13.41 kDa
Atom Count: 1,053
Modeled Residue Count: 116
Deposited Residue Count: 118
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable 2-oxoacid ferredoxin oxidoreductase, alpha chain	A	118	Thermoplasma acidophilum	Mutation(s): 0 Gene Names: Ta0773 EC: 1.2.7.11 (UniProt), 1.2.7.3 (UniProt)
UniProt
Find proteins for Q9HK35 (Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165)) Explore Q9HK35 Go to UniProtKB: Q9HK35
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9HK35
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		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: 1.90 Å
R-Value Free: 0.236 (Depositor), 0.271 (DCC)
R-Value Work: 0.198 (Depositor), 0.230 (DCC)
R-Value Observed: 0.200 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.429	α = 90
b = 65.528	β = 90
c = 72.185	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
MLPHARE	phasing
DM	model building
RESOLVE	model building
Coot	model building
ARP/wARP	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing
RESOLVE	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-09-22

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2009-09-22
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.