6PEJ

Structure of sorbitol dehydrogenase from Sinorhizobium meliloti 1021 bound to sorbitol

• PDB DOI: https://doi.org/10.2210/pdb6PEJ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Sinorhizobium meliloti 1021
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-06-20 Released: 2020-06-24 
• Deposition Author(s): Bailey-Elkin, B.A., Kohlmeier, M.G., Oresnik, I.J., Mark, B.L.
• Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.249 
• R-Value Work: 0.194 
• R-Value Observed: 0.197 

Literature

Characterization of the sorbitol dehydrogenase SmoS from Sinorhizobium meliloti 1021

Kohlmeier, M.G., Bailey-Elkin, B.A., Mark, B.L., Oresnik, I.J.

(2021) Acta Crystallogr D Biol Crystallogr 77: 380-390

• DOI: https://doi.org/10.1107/S2059798321001017

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 Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 124.02 kDa 
• Atom Count: 8,541 
• Modelled Residue Count: 1,026 
• Deposited Residue Count: 1,164 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sorbitol dehydrogenase (L-iditol 2-dehydrogenase)	A, B, C, D	291	Sinorhizobium meliloti 1021	Mutation(s): 0  Gene Names: smoS, SMc01500 EC: 1.1.1.14
UniProt
Find proteins for Q92N06 (Rhizobium meliloti (strain 1021)) Explore Q92N06  Go to UniProtKB:  Q92N06

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SOR (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth C], H [auth D]	sorbitol C6 H14 O6 FBPFZTCFMRRESA-JGWLITMVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.249 
• R-Value Work: 0.194 
• R-Value Observed: 0.197 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.298	α = 90
b = 88.298	β = 117.39
c = 87.317	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-06-24 
Deposition Author(s): Bailey-Elkin, B.A., Kohlmeier, M.G., Oresnik, I.J., Mark, B.L.

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Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	--

Revision History  

• Version 1.0: 2020-06-24
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Derived calculations, Structure summary
• Version 1.2: 2021-03-10
  Changes: Database references, Structure summary
• Version 1.3: 2023-10-11
  Changes: Data collection, Database references, Refinement description