3GG2 | pdb_00003gg2

Crystal structure of UDP-glucose 6-dehydrogenase from Porphyromonas gingivalis bound to product UDP-glucuronate

• PDB DOI: https://doi.org/10.2210/pdb3GG2/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Porphyromonas gingivalis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-02-27 Released: 2009-03-24 
• Deposition Author(s): Bonanno, J.B., Freeman, J., Bain, K.T., Chang, S., Sampathkumar, P., Wasserman, S., Sauder, J.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: 1.70 Å
• R-Value Free: 
  0.256 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.219 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Literature

Crystal structure of UDP-glucose 6-dehydrogenase from Porphyromonas gingivalis bound to product UDP-glucuronate

Bonanno, J.B., Freeman, J., Bain, K.T., Chang, S., Sampathkumar, P., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C.

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 (software)

Macromolecule Content 

• Total Structure Weight: 203.17 kDa 
• Atom Count: 14,679 
• Modeled Residue Count: 1,703 
• Deposited Residue Count: 1,800 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sugar dehydrogenase, UDP-glucose/GDP-mannose dehydrogenase family	A, B, C, D	450	Porphyromonas gingivalis	Mutation(s): 4  Gene Names: PGN_1243, PG_1143 EC: 1.1.1.22
UniProt
Find proteins for Q7MVC7 (Porphyromonas gingivalis (strain ATCC BAA-308 / W83)) Explore Q7MVC7  Go to UniProtKB:  Q7MVC7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UGA	E [auth A], F [auth A], G [auth B], H [auth C], I [auth D], J [auth D]	URIDINE-5'-DIPHOSPHATE-GLUCURONIC ACID C15 H22 N2 O18 P2 HDYANYHVCAPMJV-LXQIFKJMSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.256 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.219 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.365	α = 90
b = 143.489	β = 112.46
c = 85.501	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXCD	phasing
SHELXE	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-24 
Deposition Author(s): Bonanno, J.B., Freeman, J., Bain, K.T., Chang, S., Sampathkumar, P., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2009-03-24
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2018-11-21
  Changes: Data collection, Structure summary
• Version 1.4: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.5: 2021-10-20
  Changes: Database references
• Version 1.6: 2024-02-21
  Changes: Data collection