3W8D | pdb_00003w8d

Crystal structure of D-3-hydroxybutyrate dehydrogenase from Alcaligenes faecalis complexed with NAD+ and an inhibitor methylmalonate

• PDB DOI: https://doi.org/10.2210/pdb3W8D/pdb

• Classification: OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR
• Organism(s): Alcaligenes faecalis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-03-12 Released: 2014-03-12 
• Deposition Author(s): Kanazawa, H., Tsunoda, M., Hoque, M.M., Suzuki, K., Yamamoto, T., Takenaka, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.37 Å
• R-Value Free: 
  0.184 (Depositor), 0.182 (DCC) 
• R-Value Work: 
  0.155 (Depositor), 0.153 (DCC) 
• R-Value Observed: 
  0.158 (Depositor) 

Starting Model: experimental

Literature

X-ray diffraction of D-3-hydroxybutyrate dehydrogenase from Alcaligenes faecalis complexed with NAD+ and methylmalonate

Kanazawa, H., Tsunoda, M., Hoque, M.M., Suzuki, K., Yamamoto, T., Takenaka, A.

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: 28 kDa 
• Atom Count: 2,299 
• Modeled Residue Count: 260 
• Deposited Residue Count: 260 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-3-hydroxybutyrate dehydrogenase	A	260	Alcaligenes faecalis	Mutation(s): 0  EC: 1.1.1.30
UniProt
Find proteins for D0VWQ0 (Alcaligenes faecalis) Explore D0VWQ0  Go to UniProtKB:  D0VWQ0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	B [auth A]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
DXX	C [auth A]	METHYLMALONIC ACID C4 H6 O4 ZIYVHBGGAOATLY-UHFFFAOYSA-N
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	E [auth A], F [auth A], G [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.37 Å
• R-Value Free:  0.184 (Depositor), 0.182 (DCC) 
• R-Value Work:  0.155 (Depositor), 0.153 (DCC) 
• R-Value Observed: 0.158 (Depositor) 

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.74	α = 90
b = 62.74	β = 90
c = 119.22	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-03-12 
Deposition Author(s): Kanazawa, H., Tsunoda, M., Hoque, M.M., Suzuki, K., Yamamoto, T., Takenaka, A.

Revision History  

• Version 1.0: 2014-03-12
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description