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- PDB-8t8z: Crystal structure of Terrestrivirus Inositol pyrophosphatase kina... -

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Basic information

Entry
Database: PDB / ID: 8t8z
TitleCrystal structure of Terrestrivirus Inositol pyrophosphatase kinase in complex with ADP and myo-(1OH)IP5
ComponentsKinase
KeywordsVIRAL PROTEIN / Virus / Kinase / inositol phosphate / soil
Function / homology
Function and homology information


inositol phosphate biosynthetic process / kinase activity / ATP binding / metal ion binding
Similarity search - Function
Inositol polyphosphate kinase / Inositol polyphosphate kinase superfamily / Inositol polyphosphate kinase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Chem-ZNU / Kinase
Similarity search - Component
Biological speciesTerrestrivirus sp.
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.6 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)1ZI AES080046-31 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

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Assembly

Deposited unit
A: Kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7204
Polymers28,6891
Non-polymers1,0323
Water1,04558
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.841, 103.835, 102.719
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-538-

HOH

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Components

#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
#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-ZNU / (1S,2R,3S,4S,5S,6S)-6-hydroxycyclohexane-1,2,3,4,5-pentayl pentakis[dihydrogen (phosphate)] / myo-(1OH)IP5


Mass: 580.055 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H17O21P5 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O
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: 2.8 Å3/Da / Density % sol: 56.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
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 myo-(1OH)-IP5, 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: Oct 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 10770 / % possible obs: 99.4 % / Redundancy: 7.1 % / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.036 / Rrim(I) all: 0.098 / Χ2: 0.923 / Net I/σ(I): 8.6 / Num. measured all: 76436
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.6-2.646.90.6925550.7540.9270.2730.7480.85298.8
2.64-2.697.10.5925110.7620.930.2340.6410.86799.6
2.69-2.747.20.4955230.8230.950.1960.5360.84499.8
2.74-2.87.10.4665310.8080.9450.1870.5050.83899.8
2.8-2.867.20.3635400.9160.9780.1440.3930.86399.8
2.86-2.9370.3485340.9170.9780.1410.3780.869100
2.93-370.3255240.8950.9720.1340.3540.906100
3-3.086.90.2655270.9350.9830.110.2890.911100
3.08-3.176.50.1895460.9650.9910.080.2060.96899.5
3.17-3.285.80.1525160.9690.9920.0680.1680.92797.2
3.28-3.3970.1335390.9780.9950.0540.1440.97299.1
3.39-3.537.80.1135270.9870.9970.0440.1220.98499.8
3.53-3.697.90.0895310.9930.9980.0340.0960.97899.8
3.69-3.887.70.0685480.9960.9990.0260.0741.04399.6
3.88-4.137.70.0565340.9970.9990.0220.0610.96799.6
4.13-4.457.50.0455400.9980.9990.0180.0490.97599.6
4.45-4.897.40.0395440.99910.0150.0421.01299.3
4.89-5.67.10.0415490.9980.9990.0160.0440.85298.9
5.6-7.056.30.0445460.9980.9990.0180.0470.87997.3
7.05-5070.0246050.99910.0090.0250.90799.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
SCALEPACKdata scaling
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.6→46.38 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.907 / SU B: 8.938 / SU ML: 0.187 / Cross valid method: THROUGHOUT / ESU R: 0.453 / ESU R Free: 0.282 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2347 525 5.2 %RANDOM
Rwork0.17447 ---
obs0.17761 9615 93.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.373 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å2-0 Å20 Å2
2--0.02 Å2-0 Å2
3---0.05 Å2
Refinement stepCycle: 1 / Resolution: 2.6→46.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1772 0 60 58 1890
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0131867
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171690
X-RAY DIFFRACTIONr_angle_refined_deg1.6161.6682531
X-RAY DIFFRACTIONr_angle_other_deg1.2771.5963939
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6525216
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.17423.36798
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.52215340
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.34159
X-RAY DIFFRACTIONr_chiral_restr0.0790.2254
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022007
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02379
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_it2.883.806867
X-RAY DIFFRACTIONr_mcbond_other2.8453.8866
X-RAY DIFFRACTIONr_mcangle_it4.6025.6961082
X-RAY DIFFRACTIONr_mcangle_other4.6075.7051083
X-RAY DIFFRACTIONr_scbond_it3.8074.391000
X-RAY DIFFRACTIONr_scbond_other3.7764.379996
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.9036.3911444
X-RAY DIFFRACTIONr_long_range_B_refined7.91543.3862022
X-RAY DIFFRACTIONr_long_range_B_other7.91743.4012017
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.602→2.669 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.224 27 -
Rwork0.277 550 -
obs--72.03 %

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