3Q4W | pdb_00003q4w

The structure of archaeal inorganic pyrophosphatase in complex with substrate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • R-Value Free: 
    0.148 (DCC) 
  • R-Value Work: 
    0.117 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 3Q4W

This is version 1.5 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: https://doi.org/10.1107/S1744309112032447
  • Primary Citation 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. 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.

Macromolecule Content 

  • Total Structure Weight: 21.28 kDa 
  • Atom Count: 1,872 
  • Modeled Residue Count: 175 
  • Deposited Residue Count: 178 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Tt-IPPase178Thermococcus thioreducensMutation(s): 0 
Gene Names: Tt-IPPase
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
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
POP

Query on POP



Download:Ideal Coordinates CCD File
D [auth A]PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L
BR

Query on BR



Download:Ideal Coordinates CCD File
E [auth A]BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
CA

Query on CA



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A],
G [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
F [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • R-Value Free:  0.148 (DCC) 
  • R-Value Work:  0.117 (DCC) 
Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.046α = 90
b = 100.046β = 90
c = 98.711γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection

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: 2012-01-11
    Changes: Data collection, Experimental preparation
  • Version 1.2: 2012-02-29
    Changes: Database references
  • Version 1.3: 2014-09-17
    Changes: Database references
  • Version 1.4: 2018-01-24
    Changes: Advisory, Structure summary
  • Version 1.5: 2023-09-13
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description