3R5V

The structure of calcium bound Thermococcus thioreducens inorganic pyrophosphatase at 298K


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.122 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The structure of calcium bound Thermococcus thioreducens inorganic pyrophosphatase at 298K

Hughes, R.C.Meehan, E.J.Coates, L.Ng, J.D.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tt-IPPase
A, B, C, D, E, F
178Thermococcus thioreducensMutation(s): 0 
Gene Names: ppa
EC: 3.6.1.1
Find proteins for H0USY5 (Thermococcus thioreducens)
Go to UniProtKB:  H0USY5
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B, C, D, E, F
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MRD
Query on MRD

Download SDF File 
Download CCD File 
C, F
(4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
 Ligand Interaction
MPD
Query on MPD

Download SDF File 
Download CCD File 
C
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.122 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 106.092α = 90.00
b = 95.564β = 98.10
c = 113.769γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
HKL-2000data collection
PDB_EXTRACTdata extraction
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-03-28
    Type: Initial release
  • Version 1.1: 2017-11-08
    Type: Advisory, Derived calculations, Refinement description, Structure summary