2XAA | pdb_00002xaa

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.258 (Depositor), 0.252 (DCC) 
  • R-Value Work: 
    0.188 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 
    0.192 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history. 

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

  • DOI: https://doi.org/10.1039/c0cc00929f
  • Primary Citation 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.

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

Macromolecule Content 

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

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
SECONDARY ALCOHOL DEHYDROGENASE
A, B, C, D
345Rhodococcus ruberMutation(s): 0 
EC: 1.1.1.1
UniProt
Find proteins for Q8KLT9 (Rhodococcus ruber)
Explore Q8KLT9 
Go to UniProtKB:  Q8KLT9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8KLT9
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD

Query on NAD


Download:Ideal Coordinates CCD File
E [auth A],
H [auth B],
L [auth C],
P [auth D]		NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
BU1

Query on BU1


Download:Ideal Coordinates CCD File
J [auth B],
O [auth C],
R [auth D]		1,4-BUTANEDIOL
C4 H10 O2
WERYXYBDKMZEQL-UHFFFAOYSA-N
ZN

Query on ZN


Download:Ideal Coordinates CCD File
F [auth A]
G [auth A]
I [auth B]
K [auth B]
M [auth C]
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 (Depositor), 0.252 (DCC) 
  • R-Value Work:  0.188 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 0.192 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.674α = 90
b = 105.1β = 91.27
c = 109.176γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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