3Q3L

The neutron crystallographic structure of inorganic pyrophosphatase from Thermococcus thioreducens


Experimental Data Snapshot

  • Method: NEUTRON DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 

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This is version 1.4 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)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tt-IPPase
A, B, C, D, E, F
A, B, C, D, E, F
178Thermococcus 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupH2L2L6
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: NEUTRON DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.1α = 90
b = 95.51β = 98.08
c = 113.726γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
LAUEGENdata collection
LAUEGENdata reduction
LAUESCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-02-08
    Type: Initial release
  • Version 1.1: 2012-02-29
    Changes: Database references, Structure summary
  • Version 1.2: 2014-09-17
    Changes: Database references
  • Version 1.3: 2017-11-08
    Changes: Refinement description, Structure summary
  • Version 1.4: 2018-04-25
    Changes: Data collection