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- PDB-8jc6: Crystal structure of Mpox virus A41L protein -

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Basic information

Entry
Database: PDB / ID: 8jc6
TitleCrystal structure of Mpox virus A41L protein
ComponentsProtein OPG170
KeywordsVIRAL PROTEIN / Mpox virus
Function / homologyMajor secreted virus protein, 35kDa / Poxvirus chemokine inhibitor superfamily / Viral chemokine binding protein / extracellular region / Protein OPG170
Function and homology information
Biological speciesMonkeypox virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsJiang, H.H. / Li, J. / Zhang, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Protein Expr.Purif. / Year: 2024
Title: Expression, purification, and crystal structure of mpox virus A41 protein.
Authors: Jiang, H. / Li, J. / Jian, Y. / Yang, T. / Zhang, J. / Li, J.
History
DepositionMay 10, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 15, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Revision 1.2May 28, 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: Protein OPG170


Theoretical massNumber of molelcules
Total (without water)22,2451
Polymers22,2451
Non-polymers00
Water2,612145
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)36.505, 74.887, 77.168
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Protein OPG170


Mass: 22245.199 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Monkeypox virus / Gene: OPG170, MPXVgp151 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A7H0DND8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.37 Å3/Da / Density % sol: 48.12 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Calcium acetate hydrate, 0.1M Sodium cacodylate trihydrate pH6.5, 18% Polyethylene glycol 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jan 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.92→77.17 Å / Num. obs: 16689 / % possible obs: 99.4 % / Redundancy: 10.6 % / Biso Wilson estimate: 17.7092542416 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 26.4
Reflection shellResolution: 1.92→1.97 Å / Rmerge(I) obs: 0.134 / Num. unique obs: 1105

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PHENIX1.12_2829refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.92→38.58 Å / SU ML: 0.214515705616 / Cross valid method: NONE / σ(F): 1.34993330111 / Phase error: 25.1017561094
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.259780151648 889 5.34576067348 %
Rwork0.205752159516 15741 -
obs0.208551755156 16630 99.1415285561 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.5935164614 Å2
Refinement stepCycle: LAST / Resolution: 1.92→38.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1549 0 0 145 1694
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007130252877581582
X-RAY DIFFRACTIONf_angle_d0.9410331424942147
X-RAY DIFFRACTIONf_chiral_restr0.0606110293495244
X-RAY DIFFRACTIONf_plane_restr0.0048385004834276
X-RAY DIFFRACTIONf_dihedral_angle_d6.6615524367963
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-2.04040.2846859688661470.198957222832455X-RAY DIFFRACTION95.3113553114
2.0404-2.1980.2542235474941440.2054459374472597X-RAY DIFFRACTION100
2.198-2.41910.2903526825681720.2194166025622599X-RAY DIFFRACTION99.9639249639
2.4191-2.76910.2808166475571370.2264915362332628X-RAY DIFFRACTION100
2.7691-3.48840.2618959527931390.2131123098462670X-RAY DIFFRACTION100
3.4884-38.580.2339193123631500.1896575583282792X-RAY DIFFRACTION99.4927291173

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