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- PDB-7ypf: Crystal structure of AsfvPCNA in space group of P1 -

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Basic information

Entry
Database: PDB / ID: 7ypf
TitleCrystal structure of AsfvPCNA in space group of P1
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: 2.5 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 1.0Aug 2, 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 1.3Nov 13, 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
B: E301R
C: E301R
D: E301R
E: E301R
F: E301R


Theoretical massNumber of molelcules
Total (without water)214,9136
Polymers214,9136
Non-polymers00
Water1,982110
1
A: E301R
B: E301R
C: E301R


Theoretical massNumber of molelcules
Total (without water)107,4573
Polymers107,4573
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5580 Å2
ΔGint-13 kcal/mol
Surface area38940 Å2
MethodPISA
2
D: E301R
E: E301R
F: E301R


Theoretical massNumber of molelcules
Total (without water)107,4573
Polymers107,4573
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5550 Å2
ΔGint-12 kcal/mol
Surface area39160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.659, 118.873, 118.843
Angle α, β, γ (deg.)60.03, 89.98, 89.96
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 35818.859 Da / Num. of mol.: 6
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 3.15 Å3/Da / Density % sol: 60.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Sodium chloride, 0.1 M BICINE pH 9.0, 20% v/v PEG550

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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: 2.5→30 Å / Num. obs: 87599 / % possible obs: 97.5 % / Redundancy: 3.3 % / Biso Wilson estimate: 32.17 Å2 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.032 / Rrim(I) all: 0.061 / Χ2: 0.817 / Net I/σ(I): 11.2 / Num. measured all: 286920
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.592.80.40683930.680.280.4960.89793.3
2.59-2.693.10.32487160.810.2130.3890.93397.3
2.69-2.823.20.24287410.9030.1560.2890.91297.3
2.82-2.963.20.16887860.9790.1090.2010.91597.6
2.96-3.153.10.11985960.9720.0770.1430.91196.1
3.15-3.393.40.07989350.9880.0490.0930.88398.4
3.39-3.733.50.05588190.9920.0340.0650.82998.3
3.73-4.273.30.04288060.9940.0260.050.70998.1
4.27-5.383.60.03889070.9950.0230.0440.6899.2
5.38-303.50.03989000.9950.0240.0450.5999

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Processing

Software
NameVersionClassification
PHENIX(1.19.1_4122: ???)refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
iMOSFLMdata reduction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→29.73 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 2.05 / Phase error: 23.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2325 4429 5.27 %
Rwork0.2082 --
obs0.2094 84025 93.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→29.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13825 0 0 110 13935
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00414154
X-RAY DIFFRACTIONf_angle_d1.01919080
X-RAY DIFFRACTIONf_dihedral_angle_d8.071812
X-RAY DIFFRACTIONf_chiral_restr0.0522154
X-RAY DIFFRACTIONf_plane_restr0.0152400
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.530.26141070.25141305X-RAY DIFFRACTION47
2.53-2.560.2751740.2651653X-RAY DIFFRACTION58
2.56-2.590.3512360.26082259X-RAY DIFFRACTION76
2.59-2.620.2602740.2482643X-RAY DIFFRACTION88
2.62-2.650.25141020.23632535X-RAY DIFFRACTION93
2.65-2.690.31292120.24422640X-RAY DIFFRACTION95
2.69-2.730.28862000.2322789X-RAY DIFFRACTION96
2.73-2.770.24462400.2232611X-RAY DIFFRACTION97
2.77-2.810.25931440.22742684X-RAY DIFFRACTION97
2.81-2.860.24461670.22912820X-RAY DIFFRACTION98
2.86-2.910.30991960.23942716X-RAY DIFFRACTION97
2.91-2.960.25991530.2482733X-RAY DIFFRACTION98
2.96-3.020.27561590.22532732X-RAY DIFFRACTION97
3.02-3.080.32212000.23442676X-RAY DIFFRACTION97
3.08-3.150.21661160.22622725X-RAY DIFFRACTION95
3.15-3.220.30081690.21162848X-RAY DIFFRACTION98
3.22-3.30.22941550.20912753X-RAY DIFFRACTION99
3.3-3.390.24351190.20922880X-RAY DIFFRACTION98
3.39-3.490.24852060.21762709X-RAY DIFFRACTION98
3.49-3.60.26641200.21422816X-RAY DIFFRACTION98
3.6-3.730.2426950.19422870X-RAY DIFFRACTION99
3.73-3.880.22631480.20792805X-RAY DIFFRACTION98
3.88-4.050.20931610.19522755X-RAY DIFFRACTION98
4.05-4.270.18251600.18622764X-RAY DIFFRACTION98
4.27-4.530.12951430.15212854X-RAY DIFFRACTION99
4.54-4.880.19451680.15872780X-RAY DIFFRACTION99
4.88-5.370.29051380.19372831X-RAY DIFFRACTION99
5.37-6.140.20361170.21432843X-RAY DIFFRACTION99
6.14-7.710.26132350.23862754X-RAY DIFFRACTION99
7.72-29.730.1271150.19852813X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -8.6819 Å / Origin y: 87.8083 Å / Origin z: 53.5055 Å
111213212223313233
T0.1711 Å2-0.0157 Å2-0.0079 Å2-0.2014 Å20.0079 Å2--0.1917 Å2
L0.0515 °2-0.0708 °2-0.0372 °2-0.229 °20.1177 °2--0.1061 °2
S-0.0039 Å °-0.0005 Å °-0.0053 Å °0.0042 Å °0.0004 Å °0.0123 Å °0.0035 Å °-0.0043 Å °0.0055 Å °
Refinement TLS groupSelection details: all

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