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- PDB-8ite: Crystal structure of pE301R from African swine fever virus -

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Basic information

Entry
Database: PDB / ID: 8ite
TitleCrystal structure of pE301R from African swine fever virus
ComponentsUncharacterized protein E301R
KeywordsDNA BINDING PROTEIN / PCNA-like protein
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 / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsZhang, H. / Li, Y.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31970152 China
CitationJournal: Mbio / Year: 2023
Title: The E301R protein of African swine fever virus functions as a sliding clamp involved in viral genome replication.
Authors: Li, S. / Ge, H. / Li, Y. / Zhang, K. / Yu, S. / Cao, H. / Wang, Y. / Deng, H. / Li, J. / Dai, J. / Li, L.F. / Luo, Y. / Sun, Y. / Geng, Z. / Dong, Y. / Zhang, H. / Qiu, H.J.
History
DepositionMar 22, 2023Deposition site: PDBJ / Processing site: PDBJ
SupersessionSep 13, 2023ID: 7DRH
Revision 1.0Sep 13, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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: Uncharacterized protein E301R


Theoretical massNumber of molelcules
Total (without water)35,3001
Polymers35,3001
Non-polymers00
Water1,20767
1
A: Uncharacterized protein E301R

A: Uncharacterized protein E301R

A: Uncharacterized protein E301R

A: Uncharacterized protein E301R


Theoretical massNumber of molelcules
Total (without water)141,1984
Polymers141,1984
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
crystal symmetry operation3_645-y+1,x-1,z1
crystal symmetry operation4_665y+1,-x+1,z1
Buried area6230 Å2
ΔGint-25 kcal/mol
Surface area52490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.620, 107.620, 75.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Uncharacterized protein E301R


Mass: 35299.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) African swine fever virus / Gene: Ba71V-128, E301R / Production host: Escherichia coli (E. coli) / References: UniProt: Q65196
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 3.09 Å3/Da / Density % sol: 65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M Bis-Tris,1M sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9788 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 25053 / % possible obs: 99.5 % / Redundancy: 13.4 % / Biso Wilson estimate: 49.8 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.044 / Rrim(I) all: 0.046 / Net I/σ(I): 32.3
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 14.1 % / Rmerge(I) obs: 0.837 / Mean I/σ(I) obs: 3.43 / Num. unique obs: 1855 / CC1/2: 0.874 / Rrim(I) all: 0.91 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→19.315 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2666 1253 5 %
Rwork0.2261 --
obs0.2281 25050 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→19.315 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2270 0 0 67 2337
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012337
X-RAY DIFFRACTIONf_angle_d1.1433149
X-RAY DIFFRACTIONf_dihedral_angle_d16.6951424
X-RAY DIFFRACTIONf_chiral_restr0.068354
X-RAY DIFFRACTIONf_plane_restr0.007396
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1001-2.1840.30391390.27422634X-RAY DIFFRACTION100
2.184-2.28330.39561360.30612594X-RAY DIFFRACTION98
2.2833-2.40350.29691380.26862621X-RAY DIFFRACTION100
2.4035-2.55370.31241380.27212628X-RAY DIFFRACTION100
2.5537-2.75040.32421400.26912659X-RAY DIFFRACTION100
2.7504-3.02620.31761390.27472643X-RAY DIFFRACTION100
3.0262-3.4620.27131400.24212649X-RAY DIFFRACTION100
3.462-4.35340.27451400.20852661X-RAY DIFFRACTION100
4.3534-19.3150.21221430.18932708X-RAY DIFFRACTION100

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