1RYE | pdb_00001rye

Crystal Structure of the Shifted Form of the Glucose-Fructose Oxidoreductase from Zymomonas mobilis

• PDB DOI: https://doi.org/10.2210/pdb1RYE/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Zymomonas mobilis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-12-22 Released: 2005-02-15 
• Deposition Author(s): Kim, Y., Arora, M., Straza, M., Donnelly, M., Joachimiak, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.276 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.212 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of the Shifted Form of the Glucose-Fructose Oxidoreductase from Zymomonas mobilis

Kim, Y., Arora, M., Straza, M., Donnelly, M., Joachimiak, A.

To be published.

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: 175.51 kDa 
• Atom Count: 11,615 
• Modeled Residue Count: 1,423 
• Deposited Residue Count: 1,548 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
glucose-fructose oxidoreductase	A, B, C, D	387	Zymomonas mobilis	Mutation(s): 0  EC: 1.1.99.28
UniProt
Find proteins for Q07982 (Zymomonas mobilis subsp. mobilis (strain ATCC 31821 / ZM4 / CP4)) Explore Q07982  Go to UniProtKB:  Q07982

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDP	E [auth A], H [auth B], J [auth C], K [auth D]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N
GOL	G [auth A], I [auth B], L [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
BME	F [auth A]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.276 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.868	α = 90
b = 152.98	β = 103.66
c = 101.992	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
d*TREK	data reduction
HKL-2000	data reduction
HKL-2000	data scaling
EPMR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-02-15 
Deposition Author(s): Kim, Y., Arora, M., Straza, M., Donnelly, M., Joachimiak, A.

Revision History  

• Version 1.0: 2005-02-15
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description