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- PDB-5llb: Structure of Polyphosphate Kinase 2 from Francisella tularensis w... -

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Basic information

Entry
Database: PDB / ID: 5llb
TitleStructure of Polyphosphate Kinase 2 from Francisella tularensis with AMPPCH2PPP and polyphosphate
Components(Polyphosphate kinase ...) x 2
KeywordsTRANSFERASE / Complex with non-hydrolysable ATP analogue. Polyphosphate metabolism. Nucleotide metabolism
Function / homology
Function and homology information


phosphorus metabolic process / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a phosphate group as acceptor / polyphosphate kinase activity / metal ion binding
Similarity search - Function
Polyphosphate kinase 2, PA0141 / Polyphosphate phosphotransferase / Polyphosphate kinase-2-related / Polyphosphate kinase 2 (PPK2) / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-6YW / Chem-6YZ / ADP/GDP-polyphosphate phosphotransferase
Similarity search - Component
Biological speciesFrancisella tularensis subsp. tularensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 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 27, 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 2.0Oct 3, 2018Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / entity / pdbx_entity_nonpoly
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 2.1Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 2.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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)132,01420
Polymers127,1224
Non-polymers4,89116
Water12,106672
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7870 Å2
ΔGint-92 kcal/mol
Surface area41710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.700, 144.910, 70.590
Angle α, β, γ (deg.)90.00, 113.04, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Polyphosphate kinase ... , 2 types, 4 molecules ABCD

#1: Protein Polyphosphate kinase 2 / Uncharacterized protein


Mass: 32135.043 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. tularensis (strain SCHU S4 / Schu 4) (bacteria)
Strain: SCHU S4 / Schu 4 / Gene: ppk2, FTT_1564, BZ14_1190 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q5NEQ5, ATP-polyphosphate phosphotransferase
#2: Protein Polyphosphate kinase 2 / Uncharacterized protein


Mass: 31426.197 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. tularensis (strain SCHU S4 / Schu 4) (bacteria)
Strain: SCHU S4 / Schu 4 / Gene: ppk2, FTT_1564, BZ14_1190 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q5NEQ5, ATP-polyphosphate phosphotransferase

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Non-polymers , 5 types, 688 molecules

#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-6YZ / [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-[[oxidanyl-[oxidanyl(phosphonooxy)phosphoryl]oxy-phosphoryl]methyl]phosphinic acid


Mass: 665.168 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H20N5O18P5
#6: Chemical
ChemComp-6YW / [oxidanyl-[oxidanyl-[oxidanyl(phosphonooxy)phosphoryl]oxy-phosphoryl]oxy-phosphoryl] phosphono hydrogen phosphate


Mass: 497.895 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H8O19P6
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 672 / 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: 2.15 Å3/Da / Density % sol: 42.7 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 20 % PEG 1500, pH 8 PCTP buffer, 0.5 mM polyP, 5 mM AMPPCH2P, 10 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.92→72.46 Å / Num. obs: 82008 / % possible obs: 99.3 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 13.6

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Processing

Software
NameClassification
PHENIXrefinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CZQ

3czq


Resolution: 1.92→72.46 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.2309 3971 4.84 %3971
Rwork0.1793 ---
obs0.1818 81970 99.25 %-
Refinement stepCycle: LAST / Resolution: 1.92→72.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8039 0 264 672 8975

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