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- PDB-6lnl: ASFV core shell protein p15 -

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Basic information

Entry
Database: PDB / ID: 6lnl
TitleASFV core shell protein p15
Components60 kDa polyprotein
KeywordsVIRAL PROTEIN
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 / MOLECULAR REPLACEMENT / Resolution: 1.9286 Å
AuthorsGuo, F. / Shi, Y. / Peng, G.
CitationJournal: Faseb J. / Year: 2021
Title: The structural basis of African swine fever virus core shell protein p15 binding to DNA.
Authors: Guo, F. / Shi, Y. / Yang, M. / Guo, Y. / Shen, Z. / Li, M. / Chen, Y. / Liang, R. / Yang, Y. / Chen, H. / Peng, G.
History
DepositionDec 30, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2021Group: 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
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)57,8773
Polymers57,8773
Non-polymers00
Water5,224290
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, Static light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-23 kcal/mol
Surface area21890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.808, 57.017, 72.456
Angle α, β, γ (deg.)90.000, 116.180, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 5 through 152)
21chain B
31(chain C and resid 5 through 152)

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LYS / End label comp-ID: LYS / Auth seq-ID: 5 - 152 / Label seq-ID: 5 - 152

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1(chain A and resid 5 through 152)AA
2chain BBB
3(chain C and resid 5 through 152)CC

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Components

#1: Protein 60 kDa polyprotein


Mass: 19292.262 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) African swine fever virus / Gene: CP530R / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0A1DY09, UniProt: Q65179*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 290 / Source method: isolated from a natural source / Formula: H2O

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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: 2.05 Å3/Da / Density % sol: 39.9 %
Crystal growTemperature: 293 K / Method: evaporation / Details: 0.1 M HEPES:NaOH pH 7.5 25% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: Nonius Kappa CCD / Detector: CCD / Date: Oct 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.928→19.76 Å / Num. obs: 34865 / % possible obs: 98.38 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 14
Reflection shellResolution: 1.93→1.97 Å / Num. unique obs: 3121 / CC1/2: 0.996

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XYZ

1xyz


Resolution: 1.9286→19.7581 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.77 / Phase error: 24.64
RfactorNum. reflection% reflection
Rfree0.2191 2000 5.81 %
Rwork0.1883 --
obs0.1901 34411 97.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 78.56 Å2 / Biso mean: 36.9872 Å2 / Biso min: 17.79 Å2
Refinement stepCycle: final / Resolution: 1.9286→19.7581 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3559 0 0 290 3849
Biso mean---41.51 -
Num. residues----448
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1332X-RAY DIFFRACTION7.554TORSIONAL
12B1332X-RAY DIFFRACTION7.554TORSIONAL
13C1332X-RAY DIFFRACTION7.554TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.93-1.97680.37511200.2843194282
1.9768-2.03020.3031460.23332360100
2.0302-2.08990.28751450.2316234899
2.0899-2.15720.29031450.2214235099
2.1572-2.23420.26311440.2174234299
2.2342-2.32360.2671450.2098235599
2.3236-2.42910.24651450.2071234298
2.4291-2.55690.27291420.2166230198
2.5569-2.71680.23961450.2175236998
2.7168-2.92590.21981440.2088231798
2.9259-3.21920.22321440.2034233698
3.2192-3.68240.21951460.177236198
3.6824-4.62960.16011440.1536234898
4.6296-19.75810.17851450.1567234095

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