4DQX | pdb_00004dqx

Crystal structure of a short chain dehydrogenase from Rhizobium etli CFN 42

• PDB DOI: https://doi.org/10.2210/pdb4DQX/pdb

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


• Deposited: 2012-02-16 Released: 2012-02-29 
• Deposition Author(s): Agarwal, R., Chamala, S., Evans, B., Foti, R., Gizzi, A., Hillerich, B., Kar, A., LaFleur, J., Siedel, 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: 2.00 Å
• R-Value Free: 
  0.198 (Depositor), 0.203 (DCC) 
• R-Value Work: 
  0.159 (Depositor), 0.168 (DCC) 
• R-Value Observed: 
  0.161 (Depositor) 

Literature

Crystal structure of a short chain dehydrogenase from Rhizobium etli CFN 42

Agarwal, R., Almo, S.C., Swaminathan, S.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 119.88 kDa 
• Atom Count: 8,052 
• Modeled Residue Count: 1,006 
• Deposited Residue Count: 1,108 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable oxidoreductase protein	A, B, C, D	277	Rhizobium etli CFN 42	Mutation(s): 0  Gene Names: RHE_PD00113
UniProt
Find proteins for Q8KL31 (Rhizobium etli (strain ATCC 51251 / DSM 11541 / JCM 21823 / NBRC 15573 / CFN 42)) Explore Q8KL31  Go to UniProtKB:  Q8KL31

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.198 (Depositor), 0.203 (DCC) 
• R-Value Work:  0.159 (Depositor), 0.168 (DCC) 
• R-Value Observed: 0.161 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.245	α = 90
b = 64.595	β = 96.72
c = 113.353	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
AutoSol	phasing
Coot	model building
CCP4	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-02-29 
Deposition Author(s): Agarwal, R., Chamala, S., Evans, B., Foti, R., Gizzi, A., Hillerich, B., Kar, A., LaFleur, J., Siedel, R., Villigas, G., Zencheck, W., Almo, S.C., Swaminathan, S., New York Structural Genomics Research Consortium (NYSGRC)

Revision History  

• Version 1.0: 2012-02-29
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary