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- PDB-8xy2: Crystal structure of MPXV P1 protein S87P mutant -

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Basic information

Entry
Database: PDB / ID: 8xy2
TitleCrystal structure of MPXV P1 protein S87P mutant
ComponentsProtein OPG035
KeywordsVIRAL PROTEIN / MPXV / P1
Function / homologyOrthopoxvirus, Protein N1 / Poxvirus Bcl-2-like / Poxvirus domain superfamily / Poxvirus Bcl-2-like proteins / symbiont-mediated perturbation of host apoptosis / symbiont-mediated perturbation of host defense response / symbiont-mediated suppression of host NF-kappaB cascade / Protein OPG035
Function and homology information
Biological speciesMonkeypox virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsNi, X.C. / Lei, J.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2021YFF0702004 China
CitationJournal: Emerg Microbes Infect / Year: 2025
Title: Structural insights into MPXV P1 protein and its orthologs reveal conformational dynamics and a conserved antiviral pocket.
Authors: Ni, X. / Wang, Y. / Fan, X. / Yu, J. / Lei, J.
History
DepositionJan 19, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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

Downloads & links

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Assembly

Deposited unit
B: Protein OPG035
C: Protein OPG035
A: Protein OPG035
D: Protein OPG035


Theoretical massNumber of molelcules
Total (without water)64,7024
Polymers64,7024
Non-polymers00
Water7,062392
1
B: Protein OPG035
A: Protein OPG035


Theoretical massNumber of molelcules
Total (without water)32,3512
Polymers32,3512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-2 kcal/mol
Surface area11180 Å2
MethodPISA
2
C: Protein OPG035
D: Protein OPG035


Theoretical massNumber of molelcules
Total (without water)32,3512
Polymers32,3512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-0 kcal/mol
Surface area11290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.366, 155.500, 131.736
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Protein OPG035 / Protein N1


Mass: 16175.423 Da / Num. of mol.: 4 / Mutation: S87P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Monkeypox virus / Gene: OPG035, P1L, MPXVgp023 / Production host: Escherichia coli (E. coli) / References: UniProt: P0DTN4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 392 / 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: 2.35 Å3/Da / Density % sol: 47.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 14.4% w/v PEG 8000, 80 mM Sodium cacodylate/ Hydrochloric acid pH 6.5, 160 mM Calcium acetate, 20% v/v Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97861 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 24, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97861 Å / Relative weight: 1
ReflectionResolution: 2.24→43.91 Å / Num. obs: 29804 / % possible obs: 99.9 % / Redundancy: 6.5 % / CC1/2: 0.999 / Net I/σ(I): 11.1
Reflection shellResolution: 2.24→2.31 Å / Num. unique obs: 2712 / CC1/2: 0.949

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8XY1

8xy1


Resolution: 2.24→42.461 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.932 / SU B: 9.132 / SU ML: 0.209 / Cross valid method: FREE R-VALUE / ESU R: 0.308 / ESU R Free: 0.241
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2718 1502 5.044 %
Rwork0.2186 28274 -
all0.221 --
obs-29776 99.923 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 40.64 Å2
Baniso -1Baniso -2Baniso -3
1-3.581 Å20 Å2-0 Å2
2---0.975 Å20 Å2
3----2.605 Å2
Refinement stepCycle: LAST / Resolution: 2.24→42.461 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3875 0 0 392 4267
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133949
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173757
X-RAY DIFFRACTIONr_angle_refined_deg1.5291.6465332
X-RAY DIFFRACTIONr_angle_other_deg1.3691.5938665
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1895462
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.2221.146253
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.31215749
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4241544
X-RAY DIFFRACTIONr_chiral_restr0.0860.2512
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024355
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02893
X-RAY DIFFRACTIONr_nbd_refined0.2120.2896
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1810.23688
X-RAY DIFFRACTIONr_nbtor_refined0.1680.21975
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.21831
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.2252
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1590.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0870.212
X-RAY DIFFRACTIONr_nbd_other0.1920.274
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2420.210
X-RAY DIFFRACTIONr_mcbond_it3.8474.0581854
X-RAY DIFFRACTIONr_mcbond_other3.8454.0571853
X-RAY DIFFRACTIONr_mcangle_it5.4216.0732311
X-RAY DIFFRACTIONr_mcangle_other5.426.0742312
X-RAY DIFFRACTIONr_scbond_it4.594.482095
X-RAY DIFFRACTIONr_scbond_other4.5894.4822096
X-RAY DIFFRACTIONr_scangle_it6.8046.5453020
X-RAY DIFFRACTIONr_scangle_other6.8036.5473021
X-RAY DIFFRACTIONr_lrange_it8.42946.6974688
X-RAY DIFFRACTIONr_lrange_other8.40246.484621
X-RAY DIFFRACTIONr_ncsr_local_group_10.0790.053816
X-RAY DIFFRACTIONr_ncsr_local_group_20.1020.053716
X-RAY DIFFRACTIONr_ncsr_local_group_30.0980.053818
X-RAY DIFFRACTIONr_ncsr_local_group_40.0870.053774
X-RAY DIFFRACTIONr_ncsr_local_group_50.0770.053821
X-RAY DIFFRACTIONr_ncsr_local_group_60.0780.053779
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.24-2.2980.371190.322060X-RAY DIFFRACTION99.8168
2.298-2.3610.3551000.2992031X-RAY DIFFRACTION99.9062
2.361-2.4290.3871210.2991903X-RAY DIFFRACTION99.9506
2.429-2.5040.4221050.2991905X-RAY DIFFRACTION100
2.504-2.5860.321910.281853X-RAY DIFFRACTION99.9486
2.586-2.6770.322980.2591790X-RAY DIFFRACTION100
2.677-2.7780.292950.221723X-RAY DIFFRACTION100
2.778-2.8910.287890.2171651X-RAY DIFFRACTION100
2.891-3.0190.312890.2271581X-RAY DIFFRACTION100
3.019-3.1670.263770.231548X-RAY DIFFRACTION99.9385
3.167-3.3380.291810.2331455X-RAY DIFFRACTION99.9349
3.338-3.540.244710.2131389X-RAY DIFFRACTION99.8632
3.54-3.7830.227600.191321X-RAY DIFFRACTION100
3.783-4.0860.223540.1821221X-RAY DIFFRACTION100
4.086-4.4740.221500.1681123X-RAY DIFFRACTION100
4.474-50.209540.1471038X-RAY DIFFRACTION99.9085
5-5.770.221570.189904X-RAY DIFFRACTION100
5.77-7.0570.315400.225785X-RAY DIFFRACTION99.8789
7.057-9.940.161350.176621X-RAY DIFFRACTION99.8478
9.94-42.460.281160.247373X-RAY DIFFRACTION97.9849

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