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- PDB-7yeq: Structural insight into African Swine Fever Virus CP312R protein ... -

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Basic information

Entry
Database: PDB / ID: 7yeq
TitleStructural insight into African Swine Fever Virus CP312R protein reveals it as a single-stranded DNA binding protein
ComponentsCP312R
KeywordsVIRUS / African swine fever virus / CP312R / Single-stranded DNA binding protein / OB-fold
Function / homologyCP312R
Function and homology information
Biological speciesAfrican swine fever virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsChen, L.F. / Wu, Y.K.
Funding support China, 1items
OrganizationGrant numberCountry
Other governmentNational Natural Science Foundation of China (32002049) China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2022
Title: Structural insights into the CP312R protein of the African swine fever virus.
Authors: Chen, L. / Chen, L. / Chen, H. / Zhang, H. / Dong, P. / Sun, L. / Huang, X. / Lin, P. / Wu, L. / Jing, D. / Qian, Y. / Wu, Y.
History
DepositionJul 6, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2Feb 26, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
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: CP312R


Theoretical massNumber of molelcules
Total (without water)34,5331
Polymers34,5331
Non-polymers00
Water75742
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16540 Å2
Unit cell
Length a, b, c (Å)39.172, 66.608, 115.099
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CP312R / CP312R CDS protein / CP312R protein


Mass: 34532.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) African swine fever virus / Gene: CP312R CDS, ASFV-Georgia_4-120, CP312R / Production host: Escherichia phage EcSzw-2 (virus) / References: UniProt: A0A2X0RVH4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 2.17 Å3/Da / Density % sol: 43.43 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.15 M Potassium bromide, and 30% w/v Polyethylene glycol monomethyl ether 2,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 6, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.32→57.65 Å / Num. obs: 163761 / % possible obs: 100 % / Redundancy: 12 % / CC1/2: 0.998 / Rmerge(I) obs: 0.132 / Net I/σ(I): 11.7
Reflection shellResolution: 2.32→2.43 Å / Num. unique obs: 12840 / CC1/2: 0.9458

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.18_3845refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Alphafold2

Resolution: 2.32→33.77 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 0.02 / Phase error: 27.81 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2583 1284 10 %
Rwork0.2136 11556 -
obs0.218 12840 94.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 142.16 Å2 / Biso mean: 62.3346 Å2 / Biso min: 28.81 Å2
Refinement stepCycle: final / Resolution: 2.32→33.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2177 0 0 42 2219
Biso mean---47.4 -
Num. residues----274
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.32-2.410.34331250.3433113385
2.41-2.520.32911300.3141116588
2.52-2.650.31861330.295119588
2.65-2.820.35681400.2641125994
2.82-3.040.27771430.2548128395
3.04-3.340.2631460.2317131798
3.34-3.830.26371490.2045134899
3.83-4.820.21491550.17251389100
4.82-100.2351630.18581467100
Refinement TLS params.Method: refined / Origin x: 7.5186 Å / Origin y: -4.641 Å / Origin z: -18.7639 Å
111213212223313233
T0.3671 Å20.0219 Å2-0.0247 Å2-0.3371 Å2-0.0373 Å2--0.26 Å2
L2.5248 °2-0.0697 °20.3907 °2-3.1894 °2-0.2301 °2--0.4803 °2
S-0.093 Å °-0.188 Å °0.0467 Å °0.4716 Å °-0.0037 Å °-0.1392 Å °-0.0438 Å °-0.0868 Å °-0.0018 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA4 - 293
2X-RAY DIFFRACTION1allS1 - 43

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