4MH1 | pdb_00004mh1

Crystal structure and functional studies of quinoprotein L-sorbose dehydrogenase from Ketogulonicigenium vulgare Y25

• PDB DOI: https://doi.org/10.2210/pdb4MH1/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Ketogulonicigenium vulgare Y25
• Mutation(s): No 


• Deposited: 2013-08-29 Released: 2014-07-23 
• Deposition Author(s): Han, X., Liu, X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.232 (Depositor), 0.266 (DCC) 
• R-Value Work: 
  0.226 (Depositor), 0.217 (DCC) 
• R-Value Observed: 
  0.226 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of L-sorbose dehydrogenase, a pyrroloquinoline quinone-dependent enzyme with homodimeric assembly, from Ketogulonicigenium vulgare

Han, X., Xiong, X., Jiang, D., Chen, S., Huang, E., Zhang, W., Liu, X.

(2014) Biotechnol Lett 36: 1001-1008

• PubMed: 24557074 
• DOI: https://doi.org/10.1007/s10529-013-1446-5
• Primary Citation Related Structures: 
  4MH1


• PubMed Abstract: 
  

  The crystal structure of the L-sorbose dehydrogenase (SDH) from Ketogulonicigenium vulgare Y25 has been determined at 2.7 Å resolution using the molecular replacement method. The overall structure of SDH is similar to that of other quinoprotein dehydrogenases; consisting of an eight bladed β-propeller PQQ domain and protrusion loops. We identified a stable homodimer in crystal and demonstrated its existence in solution by sedimentation velocity measurement. By biochemical characterization of the SDH in vitro, using L-sorbose as substrate and cytochrome c551 as electron acceptor, we revealed cytochrome c551 acting as physiological primary electron acceptor for SDH.

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Organizational Affiliation: 
• State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China, [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (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: 122.9 kDa 
• Atom Count: 7,710 
• Modeled Residue Count: 1,023 
• Deposited Residue Count: 1,120 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sorbose dehydrogenase	A, B	560	Ketogulonicigenium vulgare Y25	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PQQ	C [auth B]	PYRROLOQUINOLINE QUINONE C14 H6 N2 O8 MMXZSJMASHPLLR-UHFFFAOYSA-N
CA	D [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.232 (Depositor), 0.266 (DCC) 
• R-Value Work:  0.226 (Depositor), 0.217 (DCC) 
• R-Value Observed: 0.226 (Depositor) 

Space Group: P 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 201.53	α = 90
b = 201.53	β = 90
c = 201.53	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
BALBES	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-07-23 
Deposition Author(s): Han, X., Liu, X.

Revision History  

• Version 1.0: 2014-07-23
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary