3Q4W

The structure of archaeal inorganic pyrophosphatase in complex with substrate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION

wwPDB Validation 3D Report Full Report


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 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
POP
Query on POP

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A
PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L
 Ligand Interaction
NA
Query on NA

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A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
BR
Query on BR

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Download CCD File 
A
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data collection
MOLREPphasing
DENZOdata reduction
PHENIXrefinement
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: 2012-01-11
    Type: Data collection, Experimental preparation
  • Version 1.2: 2012-02-29
    Type: Database references
  • Version 1.3: 2014-09-17
    Type: Database references
  • Version 1.4: 2018-01-24
    Type: Advisory, Structure summary