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- PDB-9h8l: Crystal Structure of Polyphosphate kinase 2-II (PPK2-II) from Lys... -

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Basic information

Entry
Database: PDB / ID: 9h8l
TitleCrystal Structure of Polyphosphate kinase 2-II (PPK2-II) from Lysinibacillus fusiformis bound to TMP
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 / PHOSPHATE ION / THYMIDINE-5'-PHOSPHATE / 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)32,4785
Polymers31,8711
Non-polymers6074
Water1,58588
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-19 kcal/mol
Surface area13120 Å2
Unit cell
Length a, b, c (Å)159.596, 159.596, 67.433
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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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-TMP / THYMIDINE-5'-PHOSPHATE


Mass: 322.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N2O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


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


Mass: 18.015 Da / Num. of mol.: 88 / 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: 3.89 Å3/Da / Density % sol: 68.38 %
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 TMP (final conc. of 0.75 M) for 24h.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.8731 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Oct 5, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 2.1→138.21 Å / Num. obs: 29017 / % possible obs: 96.6 % / Redundancy: 39.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.02 / Rrim(I) all: 0.125 / Χ2: 1.05 / Net I/σ(I): 24.8 / Num. measured all: 1138655
Reflection shellResolution: 2.1→2.16 Å / % possible obs: 100 % / Redundancy: 41.9 % / Rmerge(I) obs: 2.471 / Num. measured all: 101646 / Num. unique obs: 2424 / CC1/2: 0.763 / Rpim(I) all: 0.385 / Rrim(I) all: 2.501 / Χ2: 1.09 / Net I/σ(I) obs: 2.4

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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: 2.1→69.11 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2082 1454 5.05 %
Rwork0.1923 --
obs0.1931 28804 95.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→69.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2010 0 36 88 2134
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062118
X-RAY DIFFRACTIONf_angle_d0.7042861
X-RAY DIFFRACTIONf_dihedral_angle_d12.707822
X-RAY DIFFRACTIONf_chiral_restr0.049292
X-RAY DIFFRACTIONf_plane_restr0.006365
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.180.32441470.2682772X-RAY DIFFRACTION99
2.18-2.260.38831350.28392366X-RAY DIFFRACTION85
2.26-2.370.26081490.20932786X-RAY DIFFRACTION100
2.37-2.490.2151190.20512850X-RAY DIFFRACTION100
2.49-2.650.22781540.2082799X-RAY DIFFRACTION100
2.65-2.850.27011370.21932464X-RAY DIFFRACTION87
2.85-3.140.23121470.21032825X-RAY DIFFRACTION100
3.14-3.590.22311400.19482732X-RAY DIFFRACTION95
3.59-4.520.1751540.15452708X-RAY DIFFRACTION93
4.52-69.110.17211720.18613048X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 65.3003 Å / Origin y: 18.9995 Å / Origin z: -3.3725 Å
111213212223313233
T0.3148 Å20.0548 Å2-0.0188 Å2-0.369 Å20.0513 Å2--0.3785 Å2
L1.2301 °20.3302 °2-0.0469 °2-2.9005 °2-0.0851 °2--0.9418 °2
S-0.0888 Å °0.0538 Å °0.1764 Å °-0.113 Å °0.1384 Å °0.348 Å °-0.1736 Å °-0.1782 Å °-0.0518 Å °
Refinement TLS groupSelection details: all

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