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- PDB-8t8y: Crystal structure of Terrestrivirus inositol pyrophosphate kinase... -

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Basic information

Entry
Database: PDB / ID: 8t8y
TitleCrystal structure of Terrestrivirus inositol pyrophosphate kinase in complex with ADP and 1,4,5-InsP3
ComponentsKinase
KeywordsVIRAL PROTEIN / Virus / Kinase / inositol phosphate / soil
Function / homologyInositol polyphosphate kinase / Inositol polyphosphate kinase superfamily / Inositol polyphosphate kinase / inositol phosphate biosynthetic process / kinase activity / ADENOSINE-5'-DIPHOSPHATE / D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE / Kinase
Function and homology information
Biological speciesTerrestrivirus sp.
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.5 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 7, 2024Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.3Feb 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)29,5845
Polymers28,6891
Non-polymers8964
Water2,108117
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.619, 100.610, 105.022
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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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 / Adenosine 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.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-I3P / D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE / Inositol trisphosphate


Mass: 420.096 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15O15P3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.81 Å3/Da / Density % sol: 56.19 %
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-1,4,5-IP3, 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: Dec 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 12033 / % possible obs: 99 % / Redundancy: 8 % / CC1/2: 0.97 / CC star: 0.992 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.054 / Rrim(I) all: 0.152 / Χ2: 0.958 / Net I/σ(I): 8.5 / Num. measured all: 96592
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.5-2.548.30.8385930.8640.9630.3080.8940.955100
2.54-2.598.60.696110.9020.9740.250.7360.92699.7
2.59-2.648.90.6365770.8890.970.2240.6760.93899.8
2.64-2.698.90.5936120.8950.9720.210.630.9899.2
2.69-2.758.90.5185790.9410.9850.1840.5510.92699.8
2.75-2.828.80.4516040.9420.9850.1610.480.98499.8
2.82-2.898.80.3885830.9580.9890.1390.4130.95999.8
2.89-2.968.50.3666140.9640.9910.1340.390.965100
2.96-3.058.60.3045780.9640.9910.1110.3241.00799.8
3.05-3.158.30.2316240.9790.9950.0860.2480.972100
3.15-3.268.20.1995870.9720.9930.0750.2141.03899.8
3.26-3.397.60.1576080.9780.9940.0620.170.99199.2
3.39-3.556.60.1245970.9850.9960.0540.1360.97598.8
3.55-3.738.20.1085980.990.9970.0410.1160.93898.7
3.73-3.977.70.0875970.9930.9980.0340.0940.88997.9
3.97-4.277.30.075940.9930.9980.030.0770.82797.1
4.27-4.76.30.0555760.9950.9990.0250.0610.96795.4
4.7-5.3870.0526090.9960.9990.0230.0570.75297.6
5.38-6.787.20.0516210.9950.9990.0210.0560.67598.9
6.78-507.90.0646710.9940.9980.0250.0681.38499.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
SCALEPACKdata scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.5→37.8 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.913 / SU B: 7.416 / SU ML: 0.159 / Cross valid method: THROUGHOUT / ESU R: 0.333 / ESU R Free: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22339 606 5.1 %RANDOM
Rwork0.17334 ---
obs0.17593 11245 97.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.217 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0 Å2
2--0.02 Å20 Å2
3----0.02 Å2
Refinement stepCycle: 1 / Resolution: 2.5→37.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1764 0 53 117 1934
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0131859
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171690
X-RAY DIFFRACTIONr_angle_refined_deg1.4421.6592517
X-RAY DIFFRACTIONr_angle_other_deg1.2181.5963939
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4195216
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.76323.36798
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.27415340
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.946159
X-RAY DIFFRACTIONr_chiral_restr0.1060.2252
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022007
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_it2.3013.716867
X-RAY DIFFRACTIONr_mcbond_other2.2593.707866
X-RAY DIFFRACTIONr_mcangle_it3.8945.5551082
X-RAY DIFFRACTIONr_mcangle_other3.8945.5681083
X-RAY DIFFRACTIONr_scbond_it2.4634.021992
X-RAY DIFFRACTIONr_scbond_other2.4664.025988
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1795.8981430
X-RAY DIFFRACTIONr_long_range_B_refined7.12568.8067530
X-RAY DIFFRACTIONr_long_range_B_other7.12468.8047531
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.501→2.566 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 35 -
Rwork0.227 749 -
obs--86.92 %

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