3KLJ

Crystal structure of NADH:rubredoxin oxidoreductase from Clostridium acetobutylicum

PDB DOI: https://doi.org/10.2210/pdb3KLJ/pdb

Classification: OXIDOREDUCTASE
Organism(s): Clostridium acetobutylicum
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-11-08 Released: 2010-02-16
Deposition Author(s): Nishikawa, K., Shomura, Y., Kawasaki, S., Niimura, Y., Higuchi, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.254
R-Value Work: 0.214
R-Value Observed: 0.216

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of NADH:rubredoxin oxidoreductase from Clostridium acetobutylicum: a key component of the dioxygen scavenging system in obligatory anaerobes.

Nishikawa, K., Shomura, Y., Kawasaki, S., Niimura, Y., Higuchi, Y.

(2010) Proteins 78: 1066-1070

PubMed: 20017214 Search on PubMed
DOI: https://doi.org/10.1002/prot.22650
Primary Citation of Related Structures:
3KLJ

Organizational Affiliation

Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan.

Macromolecule Content

Total Structure Weight: 42.95 kDa
Atom Count: 3,195
Modelled Residue Count: 378
Deposited Residue Count: 385
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD(FAD)-dependent dehydrogenase, NirB-family (N-terminal domain)	A	385	Clostridium acetobutylicum	Mutation(s): 0 Gene Names: nror, CA_C2448 EC: 1.18.1.1
UniProt
Find proteins for Q9AL95 (Clostridium acetobutylicum (strain ATCC 824 / DSM 792 / JCM 1419 / LMG 5710 / VKM B-1787)) Explore Q9AL95 Go to UniProtKB: Q9AL95
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9AL95
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.254
R-Value Work: 0.214
R-Value Observed: 0.216
Space Group: P 4₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.576	α = 90
b = 98.576	β = 90
c = 88.267	γ = 90

Software Package:

Software Name	Purpose
BSS	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-02-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-02-16
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Refinement description, 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.