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 
  • R-Value Observed: 0.111 

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 Struct Biol Cryst Commun 68: 1482-1487

  • DOI: 10.1107/S1744309112032447
  • Primary Citation of Related Structures:  
    3Q3L, 3Q46, 3Q4W

  • 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 stable and is able to resist denaturation at temperatures above 348 K ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tt-IPPaseA178Thermococcus thioreducensMutation(s): 0 
Gene Names: Tt-IPPaseppa
EC: 3.6.1.1
UniProt
Find proteins for H2L2L6 (Thermococcus thioreducens)
Explore H2L2L6 
Go to UniProtKB:  H2L2L6
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download Ideal Coordinates CCD File 
G [auth A]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
B [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
H [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A], D [auth A], E [auth A], F [auth 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 
  • R-Value Observed: 0.111 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.253α = 90
b = 99.253β = 90
c = 98.557γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

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