2O3J | pdb_00002o3j

Structure of Caenorhabditis Elegans UDP-Glucose Dehydrogenase

• PDB DOI: https://doi.org/10.2210/pdb2O3J/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Caenorhabditis elegans
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-12-01 Released: 2006-12-12 
• Deposition Author(s): Zhang, Y., Zhan, C., Patskovsky, Y., Ramagopal, U., Shi, W., Toro, R., Wengerter, B.C., Milst, S., Vidal, M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free: 
  0.263 (Depositor), 0.259 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.207 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Caenorhabditis Elegans Udp-Glucose Dehydrogenase

Zhang, Y., Zhan, C., Patskovsky, Y., Ramagopal, U., Shi, W., Toro, R., Wengerter, B.C., Milstein, S., Vidal, M., Burley, S.K., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Biological Assembly 2  

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

Biological assembly 2 generated by PQS (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 159.26 kDa 
• Atom Count: 11,766 
• Modeled Residue Count: 1,389 
• Deposited Residue Count: 1,443 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-glucose 6-dehydrogenase	A, B, C	481	Caenorhabditis elegans	Mutation(s): 0  EC: 1.1.1.22
UniProt
Find proteins for Q19905 (Caenorhabditis elegans) Explore Q19905  Go to UniProtKB:  Q19905

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth A], E [auth A], F [auth A], G [auth B], H [auth B], I [auth B], J [auth C], K [auth C], L [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free:  0.263 (Depositor), 0.259 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.207 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 159.716	α = 90
b = 144.092	β = 123.24
c = 92.072	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-12-12 
Deposition Author(s): Zhang, Y., Zhan, C., Patskovsky, Y., Ramagopal, U., Shi, W., Toro, R., Wengerter, B.C., Milst, S., Vidal, M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2006-12-12
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2023-08-30
  Changes: Data collection, Database references, Refinement description