2XAA

Alcohol dehydrogenase ADH-'A' from Rhodococcus ruber DSM 44541 at pH 8.5 in complex with NAD and butane-1,4-diol

• PDB DOI: https://doi.org/10.2210/pdb2XAA/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Rhodococcus ruber
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-03-30 Released: 2010-08-11 
• Deposition Author(s): Kroutil, W., Gruber, K., Grogan, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.258 
• R-Value Work: 0.188 
• R-Value Observed: 0.192 

Starting Model: experimental

Literature

Structural Insights Into Substrate Specificity and Solvent Tolerance in Alcohol Dehydrogenase Adh-'A' from Rhodococcus Ruber Dsm 44541.

Karabec, M., Lyskowski, A., Tauber, K.C., Steinkellner, G., Kroutil, W., Grogan, G., Gruber, K.

(2010) Chem Commun (Camb) 46: 6314

• PubMed: 20676439 
• DOI: https://doi.org/10.1039/c0cc00929f
• Primary Citation of Related Structures:  
  2XAA, 3JV7


• PubMed Abstract: 
  

  The structure of the alcohol dehydrogenase ADH-'A' from Rhodococcus ruber reveals possible reasons for its remarkable tolerance to organic co-solvents and suggests new directions for structure-informed mutagenesis to produce enzymes of altered substrate specificity or improved selectivity.

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Organizational Affiliation: 

Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50/3, A-8010 Graz, Austria.

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)

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)

Macromolecule Content

• Total Structure Weight: 144.33 kDa 
• Atom Count: 10,078 
• Modelled Residue Count: 1,364 
• Deposited Residue Count: 1,380 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SECONDARY ALCOHOL DEHYDROGENASE	A, B, C, D	345	Rhodococcus ruber	Mutation(s): 0  EC: 1.1.1.1
UniProt
Find proteins for Q8KLT9 (Rhodococcus ruber) Explore Q8KLT9  Go to UniProtKB:  Q8KLT9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	E [auth A], H [auth B], L [auth C], P [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
BU1	J [auth B], O [auth C], R [auth D]	1,4-BUTANEDIOL C4 H10 O2 WERYXYBDKMZEQL-UHFFFAOYSA-N
ZN	F [auth A], G [auth A], I [auth B], K [auth B], M [auth C], N [auth C], Q [auth D], S [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.258 
• R-Value Work: 0.188 
• R-Value Observed: 0.192 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.674	α = 90
b = 105.1	β = 91.27
c = 109.176	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-08-11 
Deposition Author(s): Kroutil, W., Gruber, K., Grogan, G.

Revision History  

• Version 1.0: 2010-08-11
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description