3GG2

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


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), 0.220 (DCC) 
  • R-Value Observed: 
    0.217 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted UGAClick on this verticalbar to view details

This is version 1.6 of the entry. See complete history


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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sugar dehydrogenase, UDP-glucose/GDP-mannose dehydrogenase family
A, B, C, D
450Porphyromonas gingivalisMutation(s): 4 
Gene Names: PGN_1243PG_1143
EC: 1.1.1.22
UniProt
Find proteins for Q7MVC7 (Porphyromonas gingivalis (strain ATCC BAA-308 / W83))
Explore Q7MVC7 
Go to UniProtKB:  Q7MVC7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7MVC7
Sequence Annotations
Expand
  • Reference Sequence
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), 0.220 (DCC) 
  • R-Value Observed: 0.217 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.365α = 90
b = 143.489β = 112.46
c = 85.501γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection
MOSFLMdata reduction
SHELXCDphasing
SHELXEmodel building

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted UGAClick on this verticalbar to view details

Entry History 

Revision History  (Full details and data files)

  • 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