1RYD | pdb_00001ryd

Crystal Structure of Glucose-Fructose Oxidoreductase from Zymomonas mobilis

• PDB DOI: https://doi.org/10.2210/pdb1RYD/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., Joachimiak, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.253 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Glucose-Fructose Oxidoreductase from Zymomonas mobilis

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

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)

Macromolecule Content 

• Total Structure Weight: 88.01 kDa 
• Atom Count: 6,634 
• Modeled Residue Count: 762 
• Deposited Residue Count: 774 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
glucose-fructose oxidoreductase	A, B	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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDP	E [auth A], H [auth B]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N
GLC	F [auth B]	alpha-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-N
BME	I [auth B]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N
ACT	C [auth A], D [auth A], G [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.253 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.525	α = 90
b = 91.382	β = 90
c = 115.473	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., 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: Derived calculations, Version format compliance
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary
• Version 1.4: 2023-08-23
  Changes: Data collection, Database references, Refinement description, Structure summary