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 6N1C | pdb_00006n1c

Crystal structure of Inorganic pyrophosphatase from Legionella pneumophila Philadelphia 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.232 (Depositor), 0.235 (DCC) 
  • R-Value Work: 
    0.193 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 
    0.195 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6N1C

This is version 1.2 of the entry. See complete history. 

Literature

Characterization of a family I inorganic pyrophosphatase from Legionella pneumophila Philadelphia 1.

Moorefield, J., Konuk, Y., Norman, J.O., Abendroth, J., Edwards, T.E., Lorimer, D.D., Mayclin, S.J., Staker, B.L., Craig, J.K., Barett, K.F., Barrett, L.K., Van Voorhis, W.C., Myler, P.J., McLaughlin, K.J.

(2023) Acta Crystallogr F Struct Biol Commun 79: 257-266

  • DOI: https://doi.org/10.1107/S2053230X23008002
  • Primary Citation Related Structures: 
    6N1C

  • PubMed Abstract: 

    Inorganic pyrophosphate (PP i ) is generated as an intermediate or byproduct of many fundamental metabolic pathways, including DNA/RNA synthesis. The intracellular concentration of PP i must be regulated as buildup can inhibit many critical cellular processes. Inorganic pyrophosphatases (PPases) hydrolyze PP i into two orthophosphates (P i ), preventing the toxic accumulation of the PP i byproduct in cells and making P i available for use in biosynthetic pathways. Here, the crystal structure of a family I inorganic pyrophosphatase from Legionella pneumophila is reported at 2.0 Å resolution. L. pneumophila PPase (LpPPase) adopts a homohexameric assembly and shares the oligonucleotide/oligosaccharide-binding (OB) β-barrel core fold common to many other bacterial family I PPases. LpPPase demonstrated hydrolytic activity against a general substrate, with Mg 2+ being the preferred metal cofactor for catalysis. Legionnaires' disease is a severe respiratory infection caused primarily by L. pneumophila, and thus increased characterization of the L. pneumophila proteome is of interest.


  • Organizational Affiliation: 
    • Department of Chemistry, Vassar College, 124 Raymond Avenue, Poughkeepsie, NY 12604, USA.

Macromolecule Content 

  • Total Structure Weight: 127.95 kDa 
  • Atom Count: 8,471 
  • Modeled Residue Count: 1,029 
  • Deposited Residue Count: 1,116 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Inorganic pyrophosphatase
A, B, C, D, E
A, B, C, D, E, F
186Legionella pneumophila subsp. pneumophila str. Philadelphia 1Mutation(s): 0 
Gene Names: ppa, lpg2764
EC: 3.6.1.1
UniProt
Find proteins for Q5ZRW2 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513))
Explore Q5ZRW2 
Go to UniProtKB:  Q5ZRW2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5ZRW2
Sequence Annotations
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Reference Sequence

Small Molecules

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

Query on MPD



Download:Ideal Coordinates CCD File
I [auth A]
L [auth B]
M [auth C]
O [auth D]
Q [auth E]
I [auth A],
L [auth B],
M [auth C],
O [auth D],
Q [auth E],
R [auth E],
S [auth F]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
MRD

Query on MRD



Download:Ideal Coordinates CCD File
K [auth B](4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
ALA

Query on ALA



Download:Ideal Coordinates CCD File
J [auth A],
P [auth E]
ALANINE
C3 H7 N O2
QNAYBMKLOCPYGJ-REOHCLBHSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
G [auth A],
H [auth A],
N [auth D],
T [auth F]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.232 (Depositor), 0.235 (DCC) 
  • R-Value Work:  0.193 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 0.195 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.08α = 90
b = 119.94β = 109.59
c = 74.9γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
MoRDaphasing
ARP/wARPmodel building
BUCCANEERmodel building
Cootmodel building

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-19
    Type: Initial release
  • Version 1.1: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.2: 2024-07-17
    Changes: Database references