3Q46

Magnesium activated Inorganic pyrophosphatase from Thermococcus thioreducens bound to hydrolyzed product at 0.99 Angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.99 Å
  • R-Value Free: 0.123 
  • R-Value Work: 0.110 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Inorganic pyrophosphatase crystals from Thermococcus thioreducens for X-ray and neutron diffraction.

Hughes, R.C.Coates, L.Blakeley, M.P.Tomanicek, S.J.Langan, P.Kovalevsky, A.Y.Garcia-Ruiz, J.M.Ng, J.D.

(2012) Acta Crystallogr.,Sect.F 68: 1482-1487

  • DOI: 10.1107/S1744309112032447
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Inorganic pyrophosphatase (IPPase) from the archaeon Thermococcus thioreducens was cloned, overexpressed in Escherichia coli, purified and crystallized in restricted geometry, resulting in large crystal volumes exceeding 5 mm3. IPPase is thermally st ...

    Inorganic pyrophosphatase (IPPase) from the archaeon Thermococcus thioreducens was cloned, overexpressed in Escherichia coli, purified and crystallized in restricted geometry, resulting in large crystal volumes exceeding 5 mm3. IPPase is thermally stable and is able to resist denaturation at temperatures above 348 K. Owing to the high temperature tolerance of the enzyme, the protein was amenable to room-temperature manipulation at the level of protein preparation, crystallization and X-ray and neutron diffraction analyses. A complete synchrotron X-ray diffraction data set to 1.85 Å resolution was collected at room temperature from a single crystal of IPPase (monoclinic space group C2, unit-cell parameters a=106.11, b=95.46, c=113.68 Å, α=γ=90.0, β=98.12°). As large-volume crystals of IPPase can be obtained, preliminary neutron diffraction tests were undertaken. Consequently, Laue diffraction images were obtained, with reflections observed to 2.1 Å resolution with I/σ(I) greater than 2.5. The preliminary crystallographic results reported here set in place future structure-function and mechanism studies of IPPase.


    Organizational Affiliation

    Department of Biological Sciences and Laboratory for Structural Biology, University of Alabama in Huntsville, Huntsville, AL 35899, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tt-IPPase
A
178Thermococcus thioreducensMutation(s): 0 
Gene Names: ppa
EC: 3.6.1.1
Find proteins for H2L2L6 (Thermococcus thioreducens)
Go to UniProtKB:  H2L2L6
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

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Download CCD File 
A
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

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Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.99 Å
  • R-Value Free: 0.123 
  • R-Value Work: 0.110 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 99.253α = 90.00
b = 99.253β = 90.00
c = 98.557γ = 120.00
Software Package:
Software NamePurpose
MOLREPphasing
PHENIXrefinement
DENZOdata reduction
PDB_EXTRACTdata extraction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-01-04
    Type: Initial release
  • Version 1.1: 2012-02-29
    Type: Database references
  • Version 1.2: 2014-09-17
    Type: Database references