3KLJ | pdb_00003klj

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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.254 (Depositor), 0.276 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.241 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

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 
• DOI: https://doi.org/10.1002/prot.22650
• Primary Citation of Related Structures:  
  3KLJ

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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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

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

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 / IAM 19013 / LMG 5710 / NBRC 13948 / NRRL B-527 / VKM B-1787 / 2291 / W)) Explore Q9AL95  Go to UniProtKB:  Q9AL95

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	B [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.254 (Depositor), 0.276 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.241 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

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

Entry History 

Deposition Data

• Released Date: 2010-02-16 
Deposition Author(s): Nishikawa, K., Shomura, Y., Kawasaki, S., Niimura, Y., Higuchi, Y.

Revision History  

• Version 1.0: 2010-02-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary