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- PDB-7ype: Crystal structure of AsfvPCNA in space group of P63 -

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Basic information

Entry
Database: PDB / ID: 7ype
TitleCrystal structure of AsfvPCNA in space group of P63
ComponentsE301R
KeywordsDNA BINDING PROTEIN / sliding clamp / Proliferating cell nuclear antigen
Function / homology: / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / Uncharacterized protein E301R
Function and homology information
Biological speciesAfrican swine fever virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsShao, Z.W. / Gan, J.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: J.Virol. / Year: 2023
Title: Structural and functional studies of PCNA from African swine fever virus.
Authors: Shao, Z. / Yang, J. / Gao, Y. / Zhang, Y. / Zhao, X. / Shao, Q. / Zhang, W. / Cao, C. / Liu, H. / Gan, J.
History
DepositionAug 3, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E301R
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9112
Polymers35,8191
Non-polymers921
Water95553
1
A: E301R
hetero molecules

A: E301R
hetero molecules

A: E301R
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,7336
Polymers107,4573
Non-polymers2763
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area6350 Å2
ΔGint-12 kcal/mol
Surface area39160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.660, 118.660, 54.510
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

#1: Protein E301R / PE301R / Proliferating cell nuclear antigen-like protein / PCNA


Mass: 35818.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) African swine fever virus / Gene: E301R, AFSV47Ss_0191, ASFVARMWT4_00138 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0A1E3R5
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 3.13 Å3/Da / Density % sol: 60.65 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris pH 8.5 and 20% (w/v) PEG1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.2→29.66 Å / Num. obs: 22459 / % possible obs: 100 % / Redundancy: 18.3 % / Biso Wilson estimate: 37.98 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.03 / Rrim(I) all: 0.13 / Net I/σ(I): 18.9 / Num. measured all: 410355 / Scaling rejects: 513
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.2-2.2717.81.3633460919450.7580.3321.4032.6100
9.07-29.6619.60.03966703410.9990.0090.0463.197.4

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
Aimless0.5.29data scaling
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→29.66 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2269 1115 4.97 %
Rwork0.2089 21330 -
obs0.2098 22445 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 221.26 Å2 / Biso mean: 50.0587 Å2 / Biso min: 21 Å2
Refinement stepCycle: final / Resolution: 2.2→29.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2338 0 6 53 2397
Biso mean--82.6 44.15 -
Num. residues----286
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.2-2.30.3011410.261826472788
2.3-2.420.32041360.238326512787
2.42-2.570.28171550.248526192774
2.57-2.770.28851450.233726612806
2.77-3.050.23711350.237726562791
3.05-3.490.20531370.204626582795
3.49-4.40.18191490.186226642813
4.4-29.660.21551170.190427742891
Refinement TLS params.Method: refined / Origin x: -6.2683 Å / Origin y: -43.8052 Å / Origin z: 6.093 Å
111213212223313233
T0.2592 Å20.048 Å20.0211 Å2-0.2364 Å2-0.0035 Å2--0.2531 Å2
L4.5449 °20.8649 °20.1307 °2-0.7975 °2-0.0705 °2--0.7649 °2
S0.0951 Å °-0.0388 Å °0.3799 Å °0.0015 Å °-0.0548 Å °0.008 Å °-0.1302 Å °0.0634 Å °-0.0415 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA0 - 297
2X-RAY DIFFRACTION1allC1 - 66
3X-RAY DIFFRACTION1allB1

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