3WYE | pdb_00003wye

Crystal Structure of chimeric engineered (2S,3S)-butanediol dehydrogenase complexed with NAD+

• PDB DOI: https://doi.org/10.2210/pdb3WYE/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Klebsiella pneumoniae, Corynebacterium glutamicum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2014-08-26 Released: 2015-08-26 
• Deposition Author(s): Shimegi, T., Oyama, T., Kusunoki, M., Ui, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 
  0.199 (Depositor), 0.199 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Literature

Crystal Structure of chimeric engineered (2S,3S)-butanediol dehydrogenase complexed with NAD+

Shimegi, T., Oyama, T., Kusunoki, M., Ui, S.

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: 54.77 kDa 
• Atom Count: 3,871 
• Modeled Residue Count: 494 
• Deposited Residue Count: 512 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Diacetyl reductase [(S)-acetoin forming],L-2,3-butanediol dehydrogenase,Diacetyl reductase [(S)-acetoin forming],L-2,3-butanediol dehydrogenase,Diacetyl reductase [(S)-acetoin forming],L-2,3-butanediol dehydrogenase,Diacetyl reductase [(S)-acetoin forming]	A, B	256	Klebsiella pneumoniae, Corynebacterium glutamicum	Mutation(s): 2  Gene Names: budC EC: 1.1.1.304 (PDB Primary Data), 1.1.1.76 (PDB Primary Data)
UniProt
Find proteins for Q48436 (Klebsiella pneumoniae) Explore Q48436  Go to UniProtKB:  Q48436
Find proteins for Q9ZNN8 (Corynebacterium glutamicum) Explore Q9ZNN8  Go to UniProtKB:  Q9ZNN8
UniProt Groups	Q9ZNN8Q48436

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free:  0.199 (Depositor), 0.199 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.244	α = 90
b = 134.617	β = 90
c = 87.794	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-08-26 
Deposition Author(s): Shimegi, T., Oyama, T., Kusunoki, M., Ui, S.

Revision History  

• Version 1.0: 2015-08-26
  Type: Initial release
  
• Version 1.1: 2017-06-14
  Changes: Structure summary
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references, Derived calculations