5MIN | pdb_00005min

Apo form of the soluble PQQ-dependent Glucose Dehydrogenase from Acinetobacter calcoaceticus

• PDB DOI: https://doi.org/10.2210/pdb5MIN/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Acinetobacter calcoaceticus
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2016-11-28 Released: 2017-12-20 
• Deposition Author(s): Stines-Chaumeil, C., Mavre, F., Limoges, B., Kauffmann, B., Mano, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 
  0.214 (Depositor), 0.204 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.169 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: experimental

Literature

Apo form of the soluble PQQ-dependent Glucose Dehydrogenase from Acinetobacter calcoaceticus

Stines-Chaumeil, C., Mavre, F., Limoges, B., Kauffmann, B., Mano, N.

To be published.

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)

Macromolecule Content 

• Total Structure Weight: 100.49 kDa 
• Atom Count: 8,241 
• Modeled Residue Count: 905 
• Deposited Residue Count: 906 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Quinoprotein glucose dehydrogenase B	A, B	453	Acinetobacter calcoaceticus	Mutation(s): 0  Gene Names: gdhB EC: 1.1.5.2
UniProt
Find proteins for P13650 (Acinetobacter calcoaceticus) Explore P13650  Go to UniProtKB:  P13650

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	C [auth A], D [auth A], E [auth A], G [auth B], H [auth B], I [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free:  0.214 (Depositor), 0.204 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.169 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.407	α = 88.04
b = 54.898	β = 81.58
c = 85.474	γ = 69.62

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
XSCALE	data reduction
PHASER	phasing
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-12-20 
Deposition Author(s): Stines-Chaumeil, C., Mavre, F., Limoges, B., Kauffmann, B., Mano, N.

Revision History  

• Version 1.0: 2017-12-20
  Type: Initial release
  
• Version 1.1: 2019-10-16
  Changes: Data collection
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-23
  Changes: Structure summary