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- PDB-8t97: Crystal structure of Terrestrivirus Inositol pyrophosphatase kina... -

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Basic information

Entry
Database: PDB / ID: 8t97
TitleCrystal structure of Terrestrivirus Inositol pyrophosphatase kinase in complex with ADP and scyllo-IP6
ComponentsKinase
KeywordsVIRAL PROTEIN / Terrestrivirus / Kinase / inositol phosphate / soil
Function / homology
Function and homology information


inositol hexakisphosphate kinase activity / inositol phosphate biosynthetic process / phosphatidylinositol phosphate biosynthetic process / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Inositol polyphosphate kinase / Inositol polyphosphate kinase superfamily / Inositol polyphosphate kinase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / D-chiro inositol hexakisphosphate / PHOSPHATE ION / Kinase
Similarity search - Component
Biological speciesTerrestrivirus sp.
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.46 Å
AuthorsZong, G. / Wang, H. / Shears, S.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)1ZIAES080046-31 United States
CitationJournal: Embo J. / Year: 2024
Title: Biochemical and structural characterization of an inositol pyrophosphate kinase from a giant virus.
Authors: Zong, G. / Desfougeres, Y. / Portela-Torres, P. / Kwon, Y.U. / Saiardi, A. / Shears, S.B. / Wang, H.
History
DepositionJun 23, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 14, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8955
Polymers28,6891
Non-polymers1,2074
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.214, 103.123, 103.846
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Kinase


Mass: 28688.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Terrestrivirus sp. / Gene: Terrestrivirus9_15 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3G4ZNY6

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Non-polymers , 5 types, 71 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-KGN / D-chiro inositol hexakisphosphate


Mass: 660.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H18O24P6 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.78 Å3/Da / Density % sol: 55.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 12% PEG8000, 100mM HEPES pH 7.0, 10mM NaH2PO4, 10% Ethylene Glycol, 5mM ADP and 10mM MgCl2, then soaked in 25% PEG8000, 100mM HEPES pH 7.0, 20% Ethylene Glycol with 5mM scyllo-IP6, 5mM ADP and 10mM MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 12643 / % possible obs: 99.5 % / Redundancy: 9.1 % / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.029 / Rrim(I) all: 0.088 / Χ2: 0.993 / Net I/σ(I): 9.9 / Num. measured all: 114552
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.45-2.498.40.7186090.8720.9650.2470.7620.92798.7
2.49-2.548.60.6676260.8810.9680.2270.7081.22498.9
2.54-2.5990.6216100.8940.9720.2120.6590.91499.7
2.59-2.649.30.5616320.8990.9730.1920.5950.91299.5
2.64-2.79.40.5136060.9290.9810.1730.5430.94899.7
2.7-2.769.50.4296390.9280.9810.1450.4540.91199.7
2.76-2.839.40.3676160.9540.9880.1260.390.934100
2.83-2.99.40.3036240.970.9920.1040.3210.95599.8
2.9-2.999.30.2666380.9780.9940.0920.2820.888100
2.99-3.099.10.1996130.9840.9960.070.2110.891100
3.09-3.28.90.1556400.9890.9970.0550.1650.939100
3.2-3.328.90.1266360.9910.9980.0450.1340.88799.7
3.32-3.487.90.1016220.9930.9980.0380.1080.89599.7
3.48-3.668.80.0766250.9950.9990.0270.0810.85499.8
3.66-3.899.80.0626360.9980.9990.0210.0650.901100
3.89-4.199.70.056440.99810.0170.0530.833100
4.19-4.619.60.046480.99810.0140.0420.938100
4.61-5.289.20.046440.99810.0140.0430.80699.7
5.28-6.658.40.0466540.9970.9990.0160.0491.15998.8
6.65-508.70.0476810.9940.9990.0170.052.14297.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
SCALEPACKdata scaling
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.46→37.42 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.913 / SU B: 6.46 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R: 0.343 / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2282 603 5.2 %RANDOM
Rwork0.18022 ---
obs0.18275 11078 91.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.019 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å2-0 Å2
2---0.03 Å2-0 Å2
3---0.09 Å2
Refinement stepCycle: 1 / Resolution: 2.46→37.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1766 0 69 67 1902
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0131869
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171686
X-RAY DIFFRACTIONr_angle_refined_deg1.8411.6692536
X-RAY DIFFRACTIONr_angle_other_deg1.3341.5963929
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0475215
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.62223.36798
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.58215339
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.92159
X-RAY DIFFRACTIONr_chiral_restr0.1130.2254
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022000
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02378
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.4323.529863
X-RAY DIFFRACTIONr_mcbond_other3.4063.522862
X-RAY DIFFRACTIONr_mcangle_it5.3115.2731077
X-RAY DIFFRACTIONr_mcangle_other5.3125.2831078
X-RAY DIFFRACTIONr_scbond_it4.6524.3491006
X-RAY DIFFRACTIONr_scbond_other4.484.3998
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.9786.2681448
X-RAY DIFFRACTIONr_long_range_B_refined10.18242.2552069
X-RAY DIFFRACTIONr_long_range_B_other9.9241.8712054
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.46→2.521 Å
RfactorNum. reflection% reflection
Rfree0.291 30 -
Rwork0.244 577 -
obs--64.51 %

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