[English] 日本語
Yorodumi
- PDB-8t92: Crystal structure of Terrestrivirus Inositol pyrophosphatase kina... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8t92
TitleCrystal structure of Terrestrivirus Inositol pyrophosphatase kinase in complex with ADP and scyllo-D-(1,2,3,4)-IP4
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 / PHOSPHATE ION / Chem-XID / Kinase
Similarity search - Component
Biological speciesTerrestrivirus sp.
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.3 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7596
Polymers28,6891
Non-polymers1,0715
Water1,76598
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.532, 104.128, 103.862
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

-
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

-
Non-polymers , 5 types, 103 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.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-XID / (1S,2R,3R,4S,5R,6R)-5,6-dihydroxycyclohexane-1,2,3,4-tetrayl tetrakis[dihydrogen (phosphate)]


Mass: 500.075 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H16O18P4 / 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.: 98 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.85 %
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 D-scyllo- (1,2,3,4) ...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 D-scyllo- (1,2,3,4)IP4, 5mM ADP and 10mM MgCl2

-
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: 2.3→50 Å / Num. obs: 15183 / % possible obs: 99.2 % / Redundancy: 19.8 % / CC1/2: 0.978 / CC star: 0.994 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.034 / Rrim(I) all: 0.143 / Χ2: 1.023 / Net I/σ(I): 8.4 / Num. measured all: 299894
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.3-2.3415.60.9037500.8730.9650.2240.9330.87799.2
2.34-2.38160.8917380.8690.9640.2210.920.83599.3
2.38-2.43160.8157680.9060.9750.2050.8420.86699.4
2.43-2.4820.80.8027310.9410.9850.1780.8220.86299.9
2.48-2.5322.90.697760.9630.9910.1460.7050.883100
2.53-2.5923.40.6097340.9660.9910.1270.6220.8999.9
2.59-2.66240.547690.9770.9940.1120.5520.88599.9
2.66-2.73240.4667390.9830.9960.0970.4770.95699.9
2.73-2.8123.70.47580.9820.9950.0840.4090.9599.9
2.81-2.923.50.3187730.990.9970.0670.3250.95399.9
2.9-323.40.2897440.9850.9960.0610.2960.97100
3-3.1221.60.2237630.9880.9970.050.2291.01899.9
3.12-3.26210.1857500.990.9970.0420.191.11999.9
3.26-3.4419.20.1537630.9880.9970.0370.1581.14599.2
3.44-3.6518.20.137440.9910.9980.0320.1341.20798
3.65-3.9318.70.1077610.9920.9980.0280.1111.17999
3.93-4.33160.0947700.9930.9980.0270.0981.22698.2
4.33-4.9513.40.0827430.9920.9980.0260.0871.16996.1
4.95-6.2415.70.0847830.9940.9980.0240.0871.13398.9
6.24-5018.40.1048260.9820.9960.0270.1081.49397.8

-
Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
SCALEPACKdata scaling
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.3→37.33 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.908 / SU B: 4.991 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.237 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22845 728 5.1 %RANDOM
Rwork0.16832 ---
obs0.17142 13443 91.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.676 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å2-0 Å2
2---0.03 Å2-0 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 2.3→37.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1764 0 62 98 1924
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0131876
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171696
X-RAY DIFFRACTIONr_angle_refined_deg1.8511.6632542
X-RAY DIFFRACTIONr_angle_other_deg1.3391.5953954
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.625217
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.39723.43499
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.91115342
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.507159
X-RAY DIFFRACTIONr_chiral_restr0.1010.2254
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022018
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02380
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_it3.0232.937871
X-RAY DIFFRACTIONr_mcbond_other2.9582.93870
X-RAY DIFFRACTIONr_mcangle_it4.7534.3811087
X-RAY DIFFRACTIONr_mcangle_other4.7634.3931088
X-RAY DIFFRACTIONr_scbond_it4.6013.511005
X-RAY DIFFRACTIONr_scbond_other4.2913.482997
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.7725.0041444
X-RAY DIFFRACTIONr_long_range_B_refined8.97933.492062
X-RAY DIFFRACTIONr_long_range_B_other8.58433.2962044
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.301→2.361 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 33 -
Rwork0.204 590 -
obs--55.23 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more