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- PDB-7bq9: Crystal structure of ASFV p15 -

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Basic information

Entry
Database: PDB / ID: 7bq9
TitleCrystal structure of ASFV p15
Components60 kDa polyprotein
KeywordsSTRUCTURAL PROTEIN / ASFV / Core-shell / p15
Function / homologyviral capsid assembly / virion component / host cell perinuclear region of cytoplasm / 60 kDa polyprotein / Polyprotein pp62
Function and homology information
Biological speciesAfrican swine fever virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.612 Å
AuthorsFu, D. / Chen, C. / Guo, Y.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31941011 China
National Natural Science Foundation of China (NSFC)31670731 China
National Natural Science Foundation of China (NSFC)31870733 China
CitationJournal: Protein Cell / Year: 2020
Title: Structure of a bifunctional membrane-DNA binding protein, African swine fever virus p15
Authors: Fu, D. / Guo, Y.
History
DepositionMar 24, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: 60 kDa polyprotein
A: 60 kDa polyprotein


Theoretical massNumber of molelcules
Total (without water)43,6142
Polymers43,6142
Non-polymers00
Water00
1
A: 60 kDa polyprotein

A: 60 kDa polyprotein

A: 60 kDa polyprotein

B: 60 kDa polyprotein

B: 60 kDa polyprotein

B: 60 kDa polyprotein


Theoretical massNumber of molelcules
Total (without water)130,8436
Polymers130,8436
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation4_555x+1/2,-y+1/2,-z1
crystal symmetry operation8_555-z,x+1/2,-y+1/21
crystal symmetry operation12_555-y+1/2,-z,x+1/21
Buried area8030 Å2
ΔGint-77 kcal/mol
Surface area42620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.737, 116.737, 116.737
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213

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Components

#1: Protein 60 kDa polyprotein


Mass: 21807.086 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: SF file contains Friedel pairs. / Source: (gene. exp.) African swine fever virus / Gene: CP530R / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: A0A0A1DY09, UniProt: Q65179*PLUS
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: 3.04 Å3/Da / Density % sol: 59.53 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 2.0 M Ammonium sulfate, 0.08M BIS-TRIS propane PH 7.0, 0.22M Sodium malonate PH 7.0, 0.02M HEPES PH7.0, 0.1% v/v Jeffamine ED-2001 PH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1.07146 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07146 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 31107 / % possible obs: 99.6 % / Redundancy: 40.2 % / CC1/2: 1 / Net I/σ(I): 30.73
Reflection shellResolution: 2.61→2.76 Å / Num. unique obs: 4975 / CC1/2: 0.511

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.612→47.658 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.46
RfactorNum. reflection% reflection
Rfree0.2181 3098 9.97 %
Rwork0.1812 --
obs0.1849 31069 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 175.73 Å2 / Biso mean: 94.1074 Å2 / Biso min: 52.14 Å2
Refinement stepCycle: final / Resolution: 2.612→47.658 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2408 0 0 0 2408
Num. residues----306
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6123-2.65310.39441360.36118791
2.6531-2.69660.34761400.32811258100
2.6966-2.74310.36591480.32421238100
2.7431-2.7930.32991460.29041286100
2.793-2.84670.26951440.26171333100
2.8467-2.90480.27831380.23781226100
2.9048-2.96790.27281400.25151268100
2.9679-3.03690.3031380.27091290100
3.0369-3.11290.28191430.26691263100
3.1129-3.1970.30931420.27491267100
3.197-3.29110.34171400.26061295100
3.2911-3.39730.26551460.20951289100
3.3973-3.51870.24351420.20431272100
3.5187-3.65950.24551400.18991274100
3.6595-3.8260.21491340.18481273100
3.826-4.02760.19961400.171298100
4.0276-4.27980.16661380.1521276100
4.2798-4.610.17191420.13761257100
4.61-5.07340.17571520.14421280100
5.0734-5.80650.18771380.13871267100
5.8065-7.31130.23051400.18961278100
7.3113-47.6580.19411310.15841296100

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