4DYV | pdb_00004dyv

Crystal structure of a short-chain dehydrogenase/reductase SDR from Xanthobacter autotrophicus Py2

• PDB DOI: https://doi.org/10.2210/pdb4DYV/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Xanthobacter versatilis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-02-29 Released: 2012-03-14 
• Deposition Author(s): Agarwal, R., Chamala, S., Evans, B., Foti, R., Hillerich, B., Kar, A., Lafleur, J., Siedel, R., Villigas, G., Zencheck, W., Gizzi, A., Almo, S.C., Swaminathan, S., New York Structural Genomics Research Consortium (NYSGRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.205 (Depositor), 0.202 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.168 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Literature

Crystal structure of a short-chain dehydrogenase/reductase SDR from Xanthobacter autotrophicus Py2

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)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 29.14 kDa 
• Atom Count: 1,751 
• Modeled Residue Count: 213 
• Deposited Residue Count: 272 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Short-chain dehydrogenase/reductase SDR	A	272	Xanthobacter versatilis	Mutation(s): 0  Gene Names: Xaut_2039
UniProt
Find proteins for A7IGZ0 (Xanthobacter autotrophicus (strain ATCC BAA-1158 / Py2)) Explore A7IGZ0  Go to UniProtKB:  A7IGZ0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.205 (Depositor), 0.202 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.168 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.901	α = 90
b = 83.046	β = 90
c = 93.503	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: 2012-03-14 
Deposition Author(s): Agarwal, R., Chamala, S., Evans, B., Foti, R., Hillerich, B., Kar, A., Lafleur, J., Siedel, R., Villigas, G., Zencheck, W., Gizzi, A., Almo, S.C., Swaminathan, S., New York Structural Genomics Research Consortium (NYSGRC)

Revision History  

• Version 1.0: 2012-03-14
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary