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- PDB-9h8j: Crystal Structure of Polyphosphate kinase 2-II (PPK2-II) from Lys... -

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Basic information

Entry
Database: PDB / ID: 9h8j
TitleCrystal Structure of Polyphosphate kinase 2-II (PPK2-II) from Lysinibacillus fusiformis in apo form
ComponentsPolyphosphate kinase
KeywordsTRANSFERASE / Polyphosphate / Phosphorylation
Function / homologyPolyphosphate phosphotransferase / Polyphosphate kinase-2-related / Polyphosphate kinase 2 (PPK2) / polyphosphate kinase activity / P-loop containing nucleoside triphosphate hydrolase / PHOSPHATE ION / SUCCINIC ACID / Polyphosphate kinase
Function and homology information
Biological speciesLysinibacillus fusiformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)128,36013
Polymers127,4824
Non-polymers8789
Water8,395466
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10320 Å2
ΔGint-81 kcal/mol
Surface area42460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.112, 71.931, 97.690
Angle α, β, γ (deg.)90.00, 92.59, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Polyphosphate kinase


Mass: 31870.594 Da / Num. of mol.: 4
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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 466 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.37 Å3/Da / Density % sol: 48.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 15% (w/v) PEG 3,350, 0.1 M succinic acid pH 7.0

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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: Jun 13, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.2→66.03 Å / Num. obs: 59963 / % possible obs: 98.7 % / Redundancy: 6.9 % / CC1/2: 0.992 / Rmerge(I) obs: 0.199 / Rpim(I) all: 0.08 / Rrim(I) all: 0.215 / Χ2: 0.8 / Net I/σ(I): 8.6 / Num. measured all: 413086
Reflection shellResolution: 2.2→2.26 Å / % possible obs: 99.2 % / Redundancy: 7 % / Rmerge(I) obs: 1.255 / Num. measured all: 31313 / Num. unique obs: 4462 / CC1/2: 0.632 / Rpim(I) all: 0.51 / Rrim(I) all: 1.357 / Χ2: 0.4 / Net I/σ(I) obs: 1.4

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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: 2.2→63.13 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2527 2988 4.99 %
Rwork0.2046 --
obs0.207 59935 98.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→63.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8081 0 48 466 8595
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068307
X-RAY DIFFRACTIONf_angle_d0.89911182
X-RAY DIFFRACTIONf_dihedral_angle_d12.733193
X-RAY DIFFRACTIONf_chiral_restr0.0561153
X-RAY DIFFRACTIONf_plane_restr0.0061431
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.240.30571580.26832674X-RAY DIFFRACTION99
2.24-2.270.32031670.25312667X-RAY DIFFRACTION99
2.27-2.320.29581600.24062744X-RAY DIFFRACTION99
2.32-2.360.28811390.23852680X-RAY DIFFRACTION99
2.36-2.410.28211410.23112714X-RAY DIFFRACTION99
2.41-2.460.30721240.22992746X-RAY DIFFRACTION99
2.46-2.520.2841420.23342687X-RAY DIFFRACTION99
2.52-2.580.30851410.22652697X-RAY DIFFRACTION99
2.58-2.650.28621480.22032695X-RAY DIFFRACTION99
2.65-2.730.27661370.22032684X-RAY DIFFRACTION98
2.73-2.820.25581370.2132675X-RAY DIFFRACTION97
2.82-2.920.24541090.19892657X-RAY DIFFRACTION97
2.92-3.030.25971450.20112589X-RAY DIFFRACTION94
3.03-3.170.24021310.21092592X-RAY DIFFRACTION94
3.17-3.340.23481300.20722765X-RAY DIFFRACTION100
3.34-3.550.25651270.19692752X-RAY DIFFRACTION100
3.55-3.820.24351600.1862750X-RAY DIFFRACTION100
3.82-4.210.25231520.17662754X-RAY DIFFRACTION100
4.21-4.820.21981480.18362779X-RAY DIFFRACTION100
4.82-6.070.23191320.20192808X-RAY DIFFRACTION100
6.07-63.130.21881600.19852838X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 18.7129 Å / Origin y: 25.8967 Å / Origin z: 30.0488 Å
111213212223313233
T0.2706 Å2-0.0085 Å2-0.0189 Å2-0.2116 Å2-0.0047 Å2--0.2304 Å2
L0.8376 °2-0.2387 °2-0.2063 °2-0.7988 °2-0.0338 °2--0.49 °2
S0.0705 Å °0.1958 Å °-0.0202 Å °-0.2293 Å °-0.0549 Å °0.034 Å °-0.0341 Å °-0.0485 Å °-0.0208 Å °
Refinement TLS groupSelection details: all

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