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- PDB-5ll0: Structure of Polyphosphate Kinase 2 from Francisella tularensis S... -

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Basic information

Entry
Database: PDB / ID: 5ll0
TitleStructure of Polyphosphate Kinase 2 from Francisella tularensis SCHU S4 with polyphosphate
ComponentsPolyphosphate kinase 2
KeywordsTRANSFERASE / Polyphosphate metabolism and nucleotide metabolism / Polyphosphate Kinase 2 enzyme
Function / homology
Function and homology information


Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a phosphate group as acceptor / polyphosphate kinase activity / phosphorylation
Similarity search - Function
Polyphosphate kinase 2, PA0141 / Polyphosphate phosphotransferase / Polyphosphate kinase-2-related / Polyphosphate kinase 2 (PPK2) / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-9PI / ADP/GDP-polyphosphate phosphotransferase
Similarity search - Component
Biological speciesFrancisella tularensis subsp. tularensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsRoach, P.L. / Parnell, A.E.
Funding support United States, 1items
OrganizationGrant numberCountry
DTRAHDTRA-11-1-007 United States
Citation
Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Substrate recognition and mechanism revealed by ligand-bound polyphosphate kinase 2 structures.
Authors: Parnell, A.E. / Mordhorst, S. / Kemper, F. / Giurrandino, M. / Prince, J.P. / Schwarzer, N.J. / Hofer, A. / Wohlwend, D. / Jessen, H.J. / Gerhardt, S. / Einsle, O. / Oyston, P.C.F. / Andexer, J.N. / Roach, P.L.
#1: Journal: Biosci. Rep. / Year: 2016
Title: Biochemical and structural characterization of polyphosphate kinase 2 from the intracellular pathogen Francisella tularensis.
Authors: Batten, L.E. / Parnell, A.E. / Wells, N.J. / Murch, A.L. / Oyston, P.C. / Roach, P.L.
History
DepositionJul 25, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 11, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.4Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polyphosphate kinase 2
B: Polyphosphate kinase 2
C: Polyphosphate kinase 2
D: Polyphosphate kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,4928
Polymers128,5404
Non-polymers2,9514
Water11,025612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7140 Å2
ΔGint-39 kcal/mol
Surface area43500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.220, 145.620, 70.430
Angle α, β, γ (deg.)90.00, 113.23, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Polyphosphate kinase 2 /


Mass: 32135.043 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Polyphosphate: Nine phosphates
Source: (gene. exp.) Francisella tularensis subsp. tularensis (strain SCHU S4 / Schu 4) (bacteria)
Gene: ppk2, FTT_1564, BZ14_1190 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q5NEQ5, ATP-polyphosphate phosphotransferase
#2: Chemical
ChemComp-9PI / bis[oxidanyl-[oxidanyl-[oxidanyl(phosphonooxy)phosphoryl]oxy-phosphoryl]oxy-phosphoryl] hydrogen phosphate


Mass: 737.834 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H11O28P9
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 612 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.66 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 5 % Glycerol/PEG 4000, 0.1 M MES/imidazole pH 6.5, 0.15 M Morpheus alcohols, 1 mM polyP, 5 mM MgCl2

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92001 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92001 Å / Relative weight: 1
ReflectionResolution: 1.96→72.81 Å / Num. obs: 76026 / % possible obs: 97.1 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
xia2data reduction
xia2data scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3czq
Resolution: 1.96→59.142 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.2394 -5.03 %3819
Rwork0.1978 ---
obs0.1999 75983 96.9 %-
Solvent computationVDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.96→59.142 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8057 0 148 612 8817

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