1K2W

Crystal structure of sorbitol dehydrogenase from R. sphaeroides

• PDB DOI: https://doi.org/10.2210/pdb1K2W/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Cereibacter sphaeroides
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2001-09-29 Released: 2003-11-11 
• Deposition Author(s): Philippsen, A., Schirmer, T., Stetefeld, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.238 
• R-Value Work: 0.188 

Starting Model: experimental

Literature

Structure of zinc-independent sorbitol dehydrogenase from Rhodobacter sphaeroides at 2.4 A resolution.

Philippsen, A., Schirmer, T., Stein, M.A., Giffhorn, F., Stetefeld, J.

(2005) Acta Crystallogr D Biol Crystallogr 61: 374-379

• PubMed: 15805591 
• DOI: https://doi.org/10.1107/S0907444904034390
• Primary Citation of Related Structures:  
  1K2W


• PubMed Abstract: 
  

  Recombinant sorbitol dehydrogenase (SDH) from Rhodobacter sphaeroides has been crystallized in the absence of the cofactor NAD(H) and its structure determined to 2.4 A resolution using molecular replacement (refined R and R free factors of 18.8 and 23.8%, respectively). As expected from the sequence and shown by the conserved fold, SDH can be assigned to the short-chain dehydrogenase/reductase protein family. The cofactor NAD and the substrate sorbitol have been modelled into the structure and the active-site architecture, which displays the highly conserved catalytic tetrad of Asn-Ser-Tyr-Lys residues, is discussed in relation to the enzyme mechanism. This is the first structure of a bacterial SDH belonging to the SDR family.

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Organizational Affiliation: 

Division of Structural Biology, Biozentrum, University of Basel, Klingelbergstrasse 70, 4056 Basel, Switzerland. [e-mail]

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 Evidence: equilibrium centrifugation

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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: 54.08 kDa 
• Atom Count: 3,960 
• Modelled Residue Count: 512 
• Deposited Residue Count: 512 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SORBITOL DEHYDROGENASE	A, B	256	Cereibacter sphaeroides	Mutation(s): 0  EC: 1.1.1.14 (PDB Primary Data), 1.1.1 (UniProt), 1.1.1.16 (UniProt)
UniProt
Find proteins for Q59787 (Cereibacter sphaeroides) Explore Q59787  Go to UniProtKB:  Q59787

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.238 
• R-Value Work: 0.188 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.465	α = 90
b = 67.465	β = 90
c = 191.044	γ = 120

Software Package:

Software Name	Purpose
MOSFLM	data reduction
TRUNCATE	data reduction
AMoRE	phasing
CNS	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-11-11 
Deposition Author(s): Philippsen, A., Schirmer, T., Stetefeld, J.

Revision History  

• Version 1.0: 2003-11-11
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-25
  Changes: Advisory, Author supporting evidence
• Version 1.4: 2018-04-04
  Changes: Data collection
• Version 1.5: 2023-08-16
  Changes: Advisory, Data collection, Database references, Refinement description