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- PDB-9h8k: Crystal Structure of Polyphosphate kinase 2-II (PPK2-II) from Lys... -

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Basic information

Entry
Database: PDB / ID: 9h8k
TitleCrystal Structure of Polyphosphate kinase 2-II (PPK2-II) from Lysinibacillus fusiformis bound to AMP
ComponentsPolyphosphate kinase
KeywordsTRANSFERASE / Polyphosphate / Nucleotide / Phosphorylation
Function / homologyPolyphosphate phosphotransferase / Polyphosphate kinase-2-related / Polyphosphate kinase 2 (PPK2) / polyphosphate kinase activity / P-loop containing nucleoside triphosphate hydrolase / ADENOSINE MONOPHOSPHATE / PHOSPHATE ION / Polyphosphate kinase
Function and homology information
Biological speciesLysinibacillus fusiformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsFriedrich, F. / Kuge, M. / Keppler, M. / Gerhardt, S. / Einsle, O. / Andexer, J.N.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)527572100 Germany
CitationJournal: Chembiochem / Year: 2025
Title: Structural Insights into Broad-Range Polyphosphate Kinase 2-II Enzymes Applicable for Pyrimidine Nucleoside Diphosphate Synthesis.
Authors: Kuge, M. / Keppler, M. / Friedrich, F. / Saleem-Batcha, R. / Winter, J. / Prucker, I. / Germer, P. / Gerhardt, S. / Einsle, O. / Jung, M. / Jessen, H.J. / Andexer, J.N.
History
DepositionOct 29, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2025Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2025Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.2Mar 12, 2025Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polyphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2689
Polymers31,8711
Non-polymers1,3978
Water2,288127
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-22 kcal/mol
Surface area13690 Å2
Unit cell
Length a, b, c (Å)160.772, 160.772, 67.717
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-519-

HOH

21A-521-

HOH

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Components

#1: Protein Polyphosphate kinase


Mass: 31870.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lysinibacillus fusiformis (bacteria) / Gene: BG258_19905 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1E4R1F9
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 3.96 Å3/Da / Density % sol: 68.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.5 M ammonium sulfate, 0.1 M sodium acetate pH 4.6; Crystals have been soaked with AMP (final conc. of 0.1 M) for 24h.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Sep 13, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.1→69.62 Å / Num. obs: 30456 / % possible obs: 99.5 % / Redundancy: 38.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.243 / Rpim(I) all: 0.04 / Rrim(I) all: 0.247 / Χ2: 1.05 / Net I/σ(I): 17.7 / Num. measured all: 1171782
Reflection shellResolution: 2.1→2.16 Å / % possible obs: 94.8 % / Redundancy: 40.6 % / Rmerge(I) obs: 3.778 / Num. measured all: 94643 / Num. unique obs: 2333 / CC1/2: 0.629 / Rpim(I) all: 0.599 / Rrim(I) all: 3.826 / Χ2: 1.07 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
autoPROCdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→69.62 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2165 1469 4.83 %
Rwork0.1925 --
obs0.1937 30397 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→69.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2091 0 86 127 2304
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082245
X-RAY DIFFRACTIONf_angle_d0.7843041
X-RAY DIFFRACTIONf_dihedral_angle_d12.41891
X-RAY DIFFRACTIONf_chiral_restr0.051314
X-RAY DIFFRACTIONf_plane_restr0.007391
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.180.30871390.26322726X-RAY DIFFRACTION95
2.18-2.260.34751490.28112846X-RAY DIFFRACTION100
2.26-2.370.29471360.23872847X-RAY DIFFRACTION100
2.37-2.490.24471400.22812872X-RAY DIFFRACTION100
2.49-2.650.25131500.21492863X-RAY DIFFRACTION100
2.65-2.850.26731480.23722880X-RAY DIFFRACTION100
2.85-3.140.2411620.21972878X-RAY DIFFRACTION100
3.14-3.590.19091430.1842927X-RAY DIFFRACTION100
3.59-4.520.16861440.14182966X-RAY DIFFRACTION100
4.53-69.620.18591580.17883123X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 49.7244 Å / Origin y: -46.8472 Å / Origin z: 7.3627 Å
111213212223313233
T0.3603 Å2-0.0173 Å20.0426 Å2-0.2359 Å20.0487 Å2--0.3156 Å2
L2.1429 °20.2909 °20.0728 °2-0.939 °2-0.0234 °2--1.0115 °2
S0.0154 Å °0.2226 Å °0.3218 Å °0.0112 Å °0.0033 Å °-0.0282 Å °-0.2775 Å °0.0689 Å °-0.0223 Å °
Refinement TLS groupSelection details: all

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