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- PDB-9jvu: Crystal structure of F10 core protein from Monkeypox virus reveal... -

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Basic information

Entry
Database: PDB / ID: 9jvu
TitleCrystal structure of F10 core protein from Monkeypox virus reveals its potential inhibitors
ComponentsCore protein OPG073
KeywordsVIRAL PROTEIN / monkeypox virus / F10 core protein / crystal structure / virtual screening / viral inhibitors
Function / homologyVirion core protein, vaccinia E11L type / Chordopoxvirus E11 protein / virion component / Core protein OPG073
Function and homology information
Biological speciesMonkeypox virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsZhao, R. / Zhu, X.Y. / Cao, J.M. / Zhou, X. / Wang, D.P.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32401055 China
CitationJournal: Int.J.Biol.Macromol. / Year: 2025
Title: Crystal structure of F10 core protein from Mpox virus reveals its potential inhibitors.
Authors: Zhao, R. / Zhu, X.Y. / Zhang, J. / Xie, Z.Y. / Hu, W.S. / Han, Q.H. / Fan, J.Y. / Yang, Y.N. / Feng, B.Y. / Cao, J.M. / Zhou, X. / Wang, D.P.
History
DepositionOct 9, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 13, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Core protein OPG073


Theoretical massNumber of molelcules
Total (without water)15,3191
Polymers15,3191
Non-polymers00
Water2,450136
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.834, 69.312, 64.829
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-321-

HOH

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Components

#1: Protein Core protein OPG073 / F10 core protein


Mass: 15318.618 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Monkeypox virus / Gene: OPG073, MPXVgp059 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7H0DN46
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.3 Å3/Da / Density % sol: 46.61 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium sulfate, 0.1 M Bis-Tris, pH 5.5, and 25% w/v polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 289.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.983 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Nov 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.983 Å / Relative weight: 1
ReflectionResolution: 1.51→46.56 Å / Num. obs: 22447 / % possible obs: 99.9 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 9.2
Reflection shellResolution: 1.51→1.59 Å / Rmerge(I) obs: 0.77 / Num. unique obs: 3210

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
XDSdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6rfg

6rfg


Resolution: 1.51→34.66 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2212 1160 5.17 %
Rwork0.1871 --
obs0.1889 22420 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.51→34.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1079 0 0 136 1215
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091103
X-RAY DIFFRACTIONf_angle_d0.9471493
X-RAY DIFFRACTIONf_dihedral_angle_d19.378397
X-RAY DIFFRACTIONf_chiral_restr0.065173
X-RAY DIFFRACTIONf_plane_restr0.006188
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.51-1.580.25811330.24782618X-RAY DIFFRACTION100
1.58-1.660.28151350.21942644X-RAY DIFFRACTION100
1.66-1.770.24581500.19922598X-RAY DIFFRACTION100
1.77-1.910.21451510.17392643X-RAY DIFFRACTION100
1.91-2.10.19851490.1682645X-RAY DIFFRACTION100
2.1-2.40.21071520.17352627X-RAY DIFFRACTION100
2.4-3.020.21861360.1942701X-RAY DIFFRACTION100
3.03-34.660.22011540.18462784X-RAY DIFFRACTION100

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