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- PDB-9gp9: Crystal Structure of Polyphosphate kinase 2-II (PPK2-II) from Lys... -

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Basic information

Entry
Database: PDB / ID: 9gp9
TitleCrystal Structure of Polyphosphate kinase 2-II (PPK2-II) from Lysinibacillus fusiformis bound to ADP (form I)
ComponentsPolyphosphate kinase
KeywordsTRANSFERASE / Polyphosphate kinase 2 (PPK2) / phosphotransferase / enzyme structure / kinase / polyphosphate.
Function / homologyPolyphosphate phosphotransferase / Polyphosphate kinase-2-related / Polyphosphate kinase 2 (PPK2) / polyphosphate kinase activity / P-loop containing nucleoside triphosphate hydrolase / ADENOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / Polyphosphate kinase
Function and homology information
Biological speciesLysinibacillus fusiformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.88 Å
AuthorsSaleem-Batcha, R. / Keppler, M. / Kuge, M. / Andexer, J.N.
Funding support Germany, European Union, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)235777276/RTG1976 Germany
European Research Council (ERC)ERC project 716966European Union
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
DepositionSep 7, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)69,53410
Polymers68,1102
Non-polymers1,4248
Water724
1
A: Polyphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8626
Polymers34,0551
Non-polymers8075
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Polyphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6724
Polymers34,0551
Non-polymers6173
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.782, 109.782, 286.680
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: LEU / End label comp-ID: LEU / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 36 - 262 / Label seq-ID: 36 - 262

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Polyphosphate kinase


Mass: 34054.930 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-terminus 6X His-tagged / Source: (gene. exp.) Lysinibacillus fusiformis (bacteria) / Gene: BG258_19905 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1E4R1F9
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 3.17 Å3/Da / Density % sol: 61.21 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: Ammonium Sulfate and MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 5, 2020 / Details: Two-stage focusing X-ray optics
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.88→48.39 Å / Num. obs: 20089 / % possible obs: 99 % / Redundancy: 8.9 % / CC1/2: 0.99 / Rmerge(I) obs: 0.089 / Net I/σ(I): 16.4
Reflection shellResolution: 2.88→3.03 Å / Rmerge(I) obs: 1.5 / Num. unique obs: 2871

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.88→48.39 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.918 / SU B: 13.76 / SU ML: 0.248 / Cross valid method: FREE R-VALUE / ESU R: 0.446 / ESU R Free: 0.304
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2437 1005 5.003 %
Rwork0.1895 19084 -
all0.192 --
obs-20089 98.562 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 92.621 Å2
Baniso -1Baniso -2Baniso -3
1--0.013 Å2-0 Å2-0 Å2
2---0.013 Å20 Å2
3---0.027 Å2
Refinement stepCycle: LAST / Resolution: 2.88→48.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3341 0 84 4 3429
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0123501
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163379
X-RAY DIFFRACTIONr_angle_refined_deg1.791.8514726
X-RAY DIFFRACTIONr_angle_other_deg0.5891.7937760
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2685398
X-RAY DIFFRACTIONr_dihedral_angle_2_deg19.361526
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.59252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.5310646
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.14410170
X-RAY DIFFRACTIONr_chiral_restr0.0790.2499
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024032
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02838
X-RAY DIFFRACTIONr_nbd_refined0.2370.2696
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1990.23105
X-RAY DIFFRACTIONr_nbtor_refined0.1940.21673
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.21968
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.268
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.260.238
X-RAY DIFFRACTIONr_nbd_other0.210.2118
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3010.28
X-RAY DIFFRACTIONr_mcbond_it9.7478.5721604
X-RAY DIFFRACTIONr_mcbond_other9.7388.571604
X-RAY DIFFRACTIONr_mcangle_it12.8615.4051998
X-RAY DIFFRACTIONr_mcangle_other12.86515.4081999
X-RAY DIFFRACTIONr_scbond_it12.2129.7031897
X-RAY DIFFRACTIONr_scbond_other12.0659.6861889
X-RAY DIFFRACTIONr_scangle_it16.71117.3892728
X-RAY DIFFRACTIONr_scangle_other16.59817.3582717
X-RAY DIFFRACTIONr_lrange_it19.881107.90314811
X-RAY DIFFRACTIONr_lrange_other19.881107.9114812
X-RAY DIFFRACTIONr_ncsr_local_group_10.1090.056605
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.108530.05009
12AX-RAY DIFFRACTIONLocal ncs0.108530.05009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.88-2.9530.581720.4781362X-RAY DIFFRACTION97.551
2.953-3.0340.497710.3981359X-RAY DIFFRACTION99.7211
3.034-3.1210.284700.3421319X-RAY DIFFRACTION99.4986
3.121-3.2170.278680.2651293X-RAY DIFFRACTION99.4883
3.217-3.3220.243650.2331232X-RAY DIFFRACTION99.387
3.322-3.4380.224630.1921204X-RAY DIFFRACTION98.9071
3.438-3.5670.229620.1811172X-RAY DIFFRACTION99.2759
3.567-3.7120.236580.1711100X-RAY DIFFRACTION97.8041
3.712-3.8760.237570.1771086X-RAY DIFFRACTION99.1327
3.876-4.0640.226540.171032X-RAY DIFFRACTION98.8171
4.064-4.2820.193520.157980X-RAY DIFFRACTION98.9454
4.282-4.5390.204490.14941X-RAY DIFFRACTION99.0991
4.539-4.850.236460.142879X-RAY DIFFRACTION98.9305
4.85-5.2340.205450.152843X-RAY DIFFRACTION98.7764
5.234-5.7270.285390.167754X-RAY DIFFRACTION98.2652
5.727-6.3920.232370.211694X-RAY DIFFRACTION98.2527
6.392-7.3590.277310.228595X-RAY DIFFRACTION93.2936
7.359-8.9610.169280.155532X-RAY DIFFRACTION97.7312
8.961-12.4610.145230.139435X-RAY DIFFRACTION97.2399
12.461-48.390.45150.318272X-RAY DIFFRACTION96.3087

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