3V2H

The crystal structure of D-beta-hydroxybutyrate dehydrogenase from Sinorhizobium meliloti

• PDB DOI: https://doi.org/10.2210/pdb3V2H/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Sinorhizobium meliloti 1021
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-12-12 Released: 2011-12-28 
• Deposition Author(s): Zhang, Z., Chamala, 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: 3.00 Å
• R-Value Free: 0.286 
• R-Value Work: 0.226 
• R-Value Observed: 0.229 

Literature

The crystal structure of D-beta-hydroxybutyrate dehydrogenase from Sinorhizobium meliloti

Zhang, Z., 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 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)

Biological Assembly 4  

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

Biological assembly 4 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 60.83 kDa 
• Atom Count: 3,417 
• Modelled Residue Count: 463 
• Deposited Residue Count: 562 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-beta-hydroxybutyrate dehydrogenase	A, B	281	Sinorhizobium meliloti 1021	Mutation(s): 0  Gene Names: bdhA, RB1136, SMb21010 EC: 1.1.1.30
UniProt
Find proteins for O86034 (Rhizobium meliloti (strain 1021)) Explore O86034  Go to UniProtKB:  O86034

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: 3.00 Å
• R-Value Free: 0.286 
• R-Value Work: 0.226 
• R-Value Observed: 0.229 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.166	α = 90
b = 89.166	β = 90
c = 140.318	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-12-28 
Deposition Author(s): Zhang, Z., Chamala, 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: 2011-12-28
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2023-12-06
  Changes: Data collection