4DUP | pdb_00004dup

Crystal Structure of a quinone oxidoreductase from Rhizobium etli CFN 42

• PDB DOI: https://doi.org/10.2210/pdb4DUP/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Rhizobium etli CFN 42
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-02-22 Released: 2012-03-07 
• Deposition Author(s): Kumaran, D., Rice, S., Evans, B., Foti, R., Gizzi, A., Hillerich, B., Kar, A., Lafleur, J., Seidel, R., Villigas, G., Zencheck, W., Almo, S.C., Swaminathan, S., New York Structural Genomics Research Consortium (NYSGRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 
  0.293 (Depositor), 0.296 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.226 (DCC) 
• R-Value Observed: 
  0.225 (Depositor) 

Literature

Crystal Structure of a quinone oxidoreductase from Rhizobium etli CFN 42

Kumaran, D., Rice, S., Almo, S.C., Swaminathan, S.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 75.58 kDa 
• Atom Count: 4,821 
• Modeled Residue Count: 643 
• Deposited Residue Count: 706 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
quinone oxidoreductase	A, B	353	Rhizobium etli CFN 42	Mutation(s): 0  Gene Names: RHE_CH01141
UniProt
Find proteins for Q2KB38 (Rhizobium etli (strain ATCC 51251 / DSM 11541 / JCM 21823 / NBRC 15573 / CFN 42)) Explore Q2KB38  Go to UniProtKB:  Q2KB38

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free:  0.293 (Depositor), 0.296 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.226 (DCC) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.707	α = 90
b = 142.823	β = 90
c = 59.989	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
SHELXD	phasing
SHELXE	model building
ARP/wARP	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-03-07 
Deposition Author(s): Kumaran, D., Rice, S., Evans, B., Foti, R., Gizzi, A., Hillerich, B., Kar, A., Lafleur, J., Seidel, R., Villigas, G., Zencheck, W., Almo, S.C., Swaminathan, S., New York Structural Genomics Research Consortium (NYSGRC)

Revision History  

• Version 1.0: 2012-03-07
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary