7CDY | pdb_00007cdy

Crystal structure of glucose dehydrogenase

• PDB DOI: https://doi.org/10.2210/pdb7CDY/pdb

• Classification: HYDROLASE
• Organism(s): Serratia sp. FS14
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-06-21 Released: 2021-06-23 
• Deposition Author(s): Jia, S., Xu, D., Wang, W., Ran, T.
• Funding Organization(s): National Science Foundation (NSF, China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.33 Å
• R-Value Free: 
  0.181 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.170 (DCC) 

Starting Model: experimental

Literature

Structure of glucose dehydrogenase at 1.33 Angstroms

Jia, S., Xu, D., Wang, W., Ran, T.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 78.84 kDa 
• Atom Count: 6,495 
• Modeled Residue Count: 690 
• Deposited Residue Count: 710 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
glucose dehydrogenase	A, B	355	Serratia sp. FS14	Mutation(s): 0
UniProt
Find proteins for A0A8I3AZU9 (Serratia sp. (strain FS14)) Explore A0A8I3AZU9  Go to UniProtKB:  A0A8I3AZU9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL (Subject of Investigation/LOI)	C [auth A], E [auth B], F [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA (Subject of Investigation/LOI)	D [auth A], G [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.33 Å
• R-Value Free:  0.181 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.170 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.364	α = 90
b = 88.612	β = 106.422
c = 80.77	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-06-23 
Deposition Author(s): Jia, S., Xu, D., Wang, W., Ran, T.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	31770074
National Science Foundation (NSF, China)	China	31770050

Revision History  

• Version 1.0: 2021-06-23
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Database references, Derived calculations, Refinement description