4XA8 | pdb_00004xa8

Crystal structure of D-isomer specific 2-hydroxyacid dehydrogenase from Xanthobacter autotrophicus Py2

• PDB DOI: https://doi.org/10.2210/pdb4XA8/pdb

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


• Deposited: 2014-12-12 Released: 2015-01-14 
• Deposition Author(s): Handing, K.B., Gasiorowska, O.A., Shabalin, I.G., Cymborowski, M.T., Bonanno, J., Almo, S.C., Minor, W., New York Structural Genomics Research Consortium (NYSGRC)
• Funding Organization(s): National Institutes of Health

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.209 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.163 (Depositor), 0.173 (DCC) 
• R-Value Observed: 
  0.166 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of D-isomer specific 2-hydroxyacid dehydrogenase from Xanthobacter autotrophicus Py2.

Handing, K.B., Gasiorowska, O.A., Shabalin, I.G., Cymborowski, M.T., Bonanno, J., Almo, S.C., Minor, W., New York Structural Genomics Research Consortium (NYSGRC)

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: 34.71 kDa 
• Atom Count: 2,451 
• Modeled Residue Count: 301 
• Deposited Residue Count: 320 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding	A	320	Xanthobacter versatilis	Mutation(s): 0  Gene Names: Xaut_2571
UniProt
Find proteins for A7IIH0 (Xanthobacter versatilis) Explore A7IIH0  Go to UniProtKB:  A7IIH0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.209 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.163 (Depositor), 0.173 (DCC) 
• R-Value Observed: 0.166 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M3JG60

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.762	α = 90
b = 63.714	β = 90
c = 154.967	γ = 90

Software Package:

Software Name	Purpose
BLU-MAX	data collection
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing
HKL-3000	phasing
REFMAC	refinement
Coot	model building
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2015-01-14 
Deposition Author(s): Handing, K.B., Gasiorowska, O.A., Shabalin, I.G., Cymborowski, M.T., Bonanno, J., Almo, S.C., Minor, W., New York Structural Genomics Research Consortium (NYSGRC)

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Funding Organization	Location	Grant Number
National Institutes of Health	United States	--

Revision History  

• Version 1.0: 2015-01-14
  Type: Initial release
  
• Version 1.1: 2015-09-30
  Changes: Data collection
• Version 1.2: 2017-09-20
  Changes: Author supporting evidence, Derived calculations
• Version 1.3: 2022-04-13
  Changes: Database references, Structure summary
• Version 1.4: 2023-09-27
  Changes: Data collection, Refinement description