4OEC

Crystal structure of glycerophosphodiester phosphodiesterase from Thermococcus kodakarensis KOD1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of glycerophosphodiester phosphodiesterase from Thermococcus kodakarensis KOD1

Atsuta, Y.You, D.J.Takano, K.Koga, Y.Kanaya, S.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glycerophosphoryl diester phosphodiesteraseA, B, C, D248Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: TK1397
EC: 3.1.4.46
UniProt
Find proteins for Q5JGZ3 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
Explore Q5JGZ3 
Go to UniProtKB:  Q5JGZ3
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.724α = 90
b = 132.034β = 90
c = 171.639γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
BALBESphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-01-14
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Refinement description