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- PDB-8t8w: Crystal structure of Terrestrivirus Inositol pyrophosphatase kina... -

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Basic information

Entry
Database: PDB / ID: 8t8w
TitleCrystal structure of Terrestrivirus Inositol pyrophosphatase kinase in complex with ATP
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'-TRIPHOSPHATE / : / PHOSPHATE ION / Kinase
Similarity search - Component
Biological speciesTerrestrivirus sp.
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 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)29,7237
Polymers28,6891
Non-polymers1,0346
Water3,333185
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)63.084, 104.244, 102.402
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-536-

HOH

21A-542-

HOH

31A-660-

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-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cd / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.77 Å3/Da / Density % sol: 55.59 %
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 ATP and 2mM CdCl2

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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: Feb 12, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 23314 / % possible obs: 99.9 % / Redundancy: 12.9 % / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.021 / Rrim(I) all: 0.076 / Χ2: 0.953 / Net I/σ(I): 11.9 / Num. measured all: 300507
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2-2.0311.90.80111640.8710.9650.2380.8370.92499.9
2.03-2.0712.80.65211130.9230.980.1880.6790.92699.7
2.07-2.1113.10.54211670.9550.9880.1540.5640.94899.9
2.11-2.1513.40.44611320.9670.9920.1260.4630.963100
2.15-2.213.20.36811500.9760.9940.1040.3820.94699.9
2.2-2.2513.10.32811740.9780.9940.0930.3410.963100
2.25-2.31130.27511270.9860.9960.0790.2860.962100
2.31-2.3712.40.21311670.990.9970.0620.2220.975100
2.37-2.4411.40.1711640.9920.9980.0520.1780.93899.8
2.44-2.5213.50.15611500.9960.9990.0440.1620.97100
2.52-2.6113.70.13111430.9960.9990.0370.1360.948100
2.61-2.7113.70.11511630.9970.9990.0320.1190.965100
2.71-2.8413.50.09311680.9970.9990.0260.0960.947100
2.84-2.9913.30.08211590.9970.9990.0230.0860.97499.8
2.99-3.17130.06911710.9980.9990.020.0720.959100
3.17-3.4212.30.06111690.9980.9990.0180.0630.993100
3.42-3.7612.30.05411790.99810.0160.0571.011100
3.76-4.3113.60.05111870.99910.0150.0530.95999.9
4.31-5.43130.04912000.9960.9990.0140.0510.90899.8
5.43-5011.80.04712670.9980.9990.0150.050.87599.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
SCALEPACKdata scaling
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2→37.17 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.823 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19528 1171 5.1 %RANDOM
Rwork0.15851 ---
obs0.16038 21798 98.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.936 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2---0.02 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 2→37.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1764 0 44 185 1993
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0131901
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171704
X-RAY DIFFRACTIONr_angle_refined_deg1.7361.6482582
X-RAY DIFFRACTIONr_angle_other_deg1.4631.5863975
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0765222
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.97323.36798
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.61615343
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.005159
X-RAY DIFFRACTIONr_chiral_restr0.0860.2253
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022066
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02387
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_it2.9352.548882
X-RAY DIFFRACTIONr_mcbond_other2.9362.538881
X-RAY DIFFRACTIONr_mcangle_it4.3313.7891106
X-RAY DIFFRACTIONr_mcangle_other4.3293.8021107
X-RAY DIFFRACTIONr_scbond_it4.453.1351019
X-RAY DIFFRACTIONr_scbond_other4.3233.0971010
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.6994.4051465
X-RAY DIFFRACTIONr_long_range_B_refined9.97431.7462250
X-RAY DIFFRACTIONr_long_range_B_other9.56530.5952183
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.048 Å
RfactorNum. reflection% reflection
Rfree0.252 63 -
Rwork0.239 1371 -
obs--84.55 %

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