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- PDB-8xy3: Crystal structure of VARV P1 protein -

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Basic information

Entry
Database: PDB / ID: 8xy3
TitleCrystal structure of VARV P1 protein
ComponentsP1L
KeywordsVIRAL PROTEIN / VARV / P1
Function / homologyOrthopoxvirus, Protein N1 / Poxvirus Bcl-2-like / Poxvirus domain superfamily / Poxvirus Bcl-2-like proteins / symbiont-mediated perturbation of host apoptosis / : / R1L protein
Function and homology information
Biological speciesVariola virus (smallpox virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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
C: P1L
B: P1L
D: P1L
A: P1L


Theoretical massNumber of molelcules
Total (without water)64,4054
Polymers64,4054
Non-polymers00
Water4,576254
1
C: P1L
D: P1L


Theoretical massNumber of molelcules
Total (without water)32,2032
Polymers32,2032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-2 kcal/mol
Surface area11130 Å2
MethodPISA
2
B: P1L
A: P1L


Theoretical massNumber of molelcules
Total (without water)32,2032
Polymers32,2032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-2 kcal/mol
Surface area11040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.064, 153.786, 132.146
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11D-256-

HOH

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Components

#1: Protein
P1L


Mass: 16101.294 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Variola virus (smallpox virus) / Gene: R1L / Production host: Escherichia coli (E. coli) / References: UniProt: Q76Q58
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 2.33 Å3/Da / Density % sol: 47.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Calcium chloride dihydrate, 0.1 M Tris pH 8.0, 20% w/v PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 8, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.2→132.15 Å / Num. obs: 31040 / % possible obs: 100 % / Redundancy: 12.6 % / CC1/2: 0.993 / Net I/σ(I): 11.4
Reflection shellResolution: 2.2→2.27 Å / Num. unique obs: 2655 / CC1/2: 0.978

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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: 2.2→66.16 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.938 / SU B: 7.327 / SU ML: 0.173 / Cross valid method: FREE R-VALUE / ESU R: 0.259 / ESU R Free: 0.202
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2408 1515 4.886 %
Rwork0.2038 29489 -
all0.206 --
obs-31004 99.932 %
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: 44.245 Å2
Baniso -1Baniso -2Baniso -3
1-4.588 Å20 Å2-0 Å2
2---1.884 Å20 Å2
3----2.704 Å2
Refinement stepCycle: LAST / Resolution: 2.2→66.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3903 0 0 254 4157
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133969
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173740
X-RAY DIFFRACTIONr_angle_refined_deg1.4731.6425362
X-RAY DIFFRACTIONr_angle_other_deg1.3221.5858638
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2855468
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.83321.694248
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.05615746
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7111540
X-RAY DIFFRACTIONr_chiral_restr0.0790.2515
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024386
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02870
X-RAY DIFFRACTIONr_nbd_refined0.2060.2806
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1770.23625
X-RAY DIFFRACTIONr_nbtor_refined0.1650.21913
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.21795
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2223
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2570.28
X-RAY DIFFRACTIONr_nbd_other0.2150.253
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2130.29
X-RAY DIFFRACTIONr_mcbond_it3.5844.4621884
X-RAY DIFFRACTIONr_mcbond_other3.5844.461883
X-RAY DIFFRACTIONr_mcangle_it5.1146.6812348
X-RAY DIFFRACTIONr_mcangle_other5.1136.6832349
X-RAY DIFFRACTIONr_scbond_it4.4664.9032085
X-RAY DIFFRACTIONr_scbond_other4.4654.9042086
X-RAY DIFFRACTIONr_scangle_it6.7517.1683014
X-RAY DIFFRACTIONr_scangle_other6.7517.173015
X-RAY DIFFRACTIONr_lrange_it8.29450.4374524
X-RAY DIFFRACTIONr_lrange_other8.30250.3344493
X-RAY DIFFRACTIONr_ncsr_local_group_10.0870.053894
X-RAY DIFFRACTIONr_ncsr_local_group_20.0880.053750
X-RAY DIFFRACTIONr_ncsr_local_group_30.0870.053690
X-RAY DIFFRACTIONr_ncsr_local_group_40.0960.053712
X-RAY DIFFRACTIONr_ncsr_local_group_50.10.053677
X-RAY DIFFRACTIONr_ncsr_local_group_60.0830.053760
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2570.3761070.2992174X-RAY DIFFRACTION99.9124
2.257-2.3190.3041050.2952054X-RAY DIFFRACTION99.9537
2.319-2.3860.2751090.2792049X-RAY DIFFRACTION99.7688
2.386-2.4590.271920.2722008X-RAY DIFFRACTION100
2.459-2.540.311010.261913X-RAY DIFFRACTION100
2.54-2.6290.289870.2441862X-RAY DIFFRACTION100
2.629-2.7280.3980.2091811X-RAY DIFFRACTION100
2.728-2.8390.24850.2181739X-RAY DIFFRACTION100
2.839-2.9650.318840.2131656X-RAY DIFFRACTION99.9426
2.965-3.110.248980.2191600X-RAY DIFFRACTION100
3.11-3.2780.269920.2211502X-RAY DIFFRACTION99.9373
3.278-3.4760.229710.2091446X-RAY DIFFRACTION99.9341
3.476-3.7160.263660.2031361X-RAY DIFFRACTION100
3.716-4.0130.213690.1721259X-RAY DIFFRACTION100
4.013-4.3950.176540.1551182X-RAY DIFFRACTION100
4.395-4.9110.169570.1551075X-RAY DIFFRACTION100
4.911-5.6670.216450.163947X-RAY DIFFRACTION100
5.667-6.9320.189460.182816X-RAY DIFFRACTION100
6.932-9.7630.134270.162658X-RAY DIFFRACTION100
9.763-66.160.311220.22377X-RAY DIFFRACTION97.555

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