4KUG | pdb_00004kug

Crystal structure of 3-hydroxybutylryl-CoA dehydrogenase with NAD from Clostridium butyricum

• PDB DOI: https://doi.org/10.2210/pdb4KUG/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Clostridium butyricum E4 str. BoNT E BL5262
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-05-22 Released: 2014-05-28 
• Deposition Author(s): Kim, E.J., Kim, S., Kim, K.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.281 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.221 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of (S)-3-hydroxybutylryl-CoA dehydrogenase form the n-butanol sysnthesizing bacterium, Clostridium butyricum

Kim, E.J., Kim, S., Kim, K.J.

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 128.81 kDa 
• Atom Count: 8,910 
• Modeled Residue Count: 1,128 
• Deposited Residue Count: 1,160 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-hydroxybutyryl-CoA dehydrogenase	A, B, C, D	290	Clostridium butyricum E4 str. BoNT E BL5262	Mutation(s): 0  Gene Names: hbd, CLP_3850 EC: 1.1.1.157
UniProt
Find proteins for C4IEM5 (Clostridium butyricum E4 str. BoNT E BL5262) Explore C4IEM5  Go to UniProtKB:  C4IEM5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	E [auth A], F [auth B], G [auth C], H [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.281 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 148.45	α = 90
b = 148.45	β = 90
c = 201.63	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-05-28 
Deposition Author(s): Kim, E.J., Kim, S., Kim, K.J.

Revision History  

• Version 1.0: 2014-05-28
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description