1G6K | pdb_00001g6k

Crystal structure of glucose dehydrogenase mutant E96A complexed with NAD+

• PDB DOI: https://doi.org/10.2210/pdb1G6K/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Priestia megaterium
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2000-11-06 Released: 2003-08-12 
• Deposition Author(s): Yamamoto, K., Kurisu, G., Kusunoki, M., Tabata, S., Urabe, I., Osaki, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.238 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.220 (DCC) 

Starting Model: experimental

Literature

Structural analysis of stability-increasing mutants of glucose dehydrogenase

Yamamoto, K., Kurisu, G., Kusunoki, M., Tabata, S., Urabe, I., Osaki, S.

To be published.

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,PQS (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 114.87 kDa 
• Atom Count: 8,359 
• Modeled Residue Count: 1,044 
• Deposited Residue Count: 1,044 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLUCOSE 1-DEHYDROGENASE	A, B, C [auth E], D [auth F]	261	Priestia megaterium	Mutation(s): 1  EC: 1.1.1.47
UniProt
Find proteins for P40288 (Priestia megaterium) Explore P40288  Go to UniProtKB:  P40288

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	E [auth A], F [auth B], G [auth E], H [auth F]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.238 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.220 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.955	α = 90
b = 66.64	β = 93.44
c = 120.065	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-08-12 
Deposition Author(s): Yamamoto, K., Kurisu, G., Kusunoki, M., Tabata, S., Urabe, I., Osaki, S.

Revision History  

• Version 1.0: 2003-08-12
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2021-11-10
  Changes: Database references, Derived calculations
• Version 1.4: 2023-10-25
  Changes: Data collection, Refinement description