4LSW

Crystallization and Structural Analysis of 2-Hydroxyacid Dehydrogenase from Ketogulonicigenium vulgare Y25

• PDB DOI: https://doi.org/10.2210/pdb4LSW/pdb

• Classification: HYDROLASE
• Organism(s): Ketogulonicigenium vulgare Y25
• Mutation(s): No 


• Deposited: 2013-07-23 Released: 2013-09-11 
• Deposition Author(s): Han, X., Liu, X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 0.251 
• R-Value Work: 0.211 
• R-Value Observed: 0.213 

Literature

Crystallization and structural analysis of 2-hydroxyacid dehydrogenase from Ketogulonicigenium vulgare.

Han, X., Xiong, X., Hu, X., Li, M., Zhang, W., Liu, X.

(2014) Biotechnol Lett 36: 295-300

• PubMed: 24068509 
• DOI: https://doi.org/10.1007/s10529-013-1354-8
• Primary Citation of Related Structures:  
  4LSW


• PubMed Abstract: 
  

  L-2-Hydroxyacid dehydrogenase (HDH) from Ketogulonicigenium vulgare Y25 was cloned and overexpressed in Escherichia coli. The protein was purified and crystallized by the sitting-drop vapour-diffusion method with polyethylene glycol 3350 as precipitant. The crystal structure of HDH was determined at 1.64 Å resolution using the molecular replacement method with the crystal structure of hydroxyl (phenyl) pyruvate reductase from Coleus blumei Benth as the search model. The overall structure of HDH was similar to that of hydroxyl(phenyl)pyruvate reductase, consisting of two compact domains separated by a deep active cleft. The most significant structural divergence is located around the pocket gate comprising residues A210, T211 and R212, which is located on top of the catalytic triad.

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Organizational Affiliation: 

State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China, [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 34.39 kDa 
• Atom Count: 2,849 
• Modelled Residue Count: 318 
• Deposited Residue Count: 318 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-2-hydroxyacid dehydrogensase protein	A	318	Ketogulonicigenium vulgare Y25	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 0.251 
• R-Value Work: 0.211 
• R-Value Observed: 0.213 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.202	α = 90
b = 52.333	β = 107.46
c = 65.647	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASES	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-09-11 
Deposition Author(s): Han, X., Liu, X.

Revision History  

• Version 1.0: 2013-09-11
  Type: Initial release
  
• Version 1.1: 2015-06-17
  Changes: Database references
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description