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- PDB-8i6h: Crystal structure of the African swine fever virus DNA sliding cl... -

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Basic information

Entry
Database: PDB / ID: 8i6h
TitleCrystal structure of the African swine fever virus DNA sliding clamp (selenomethionine form)
ComponentsASFV DNA sliding clamp
KeywordsDNA BINDING PROTEIN / DNA polymerase processivity factor / sliding clamp
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 BA71V
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.292 Å
AuthorsWu, J. / Gong, P.
Funding support China, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2022YFC2303300 China
National Natural Science Foundation of China (NSFC)32000136 China
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Crystal structure of African swine fever virus pE301R reveals a ring-shaped trimeric DNA sliding clamp.
Authors: Wu, J. / Zheng, H. / Gong, P.
History
DepositionJan 28, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 12, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _pdbx_initial_refinement_model.type
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ASFV DNA sliding clamp
B: ASFV DNA sliding clamp


Theoretical massNumber of molelcules
Total (without water)73,6442
Polymers73,6442
Non-polymers00
Water2,234124
1
A: ASFV DNA sliding clamp

A: ASFV DNA sliding clamp

A: ASFV DNA sliding clamp


Theoretical massNumber of molelcules
Total (without water)110,4663
Polymers110,4663
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area5270 Å2
ΔGint-16 kcal/mol
Surface area34960 Å2
MethodPISA
2
B: ASFV DNA sliding clamp

B: ASFV DNA sliding clamp

B: ASFV DNA sliding clamp


Theoretical massNumber of molelcules
Total (without water)110,4663
Polymers110,4663
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area5270 Å2
ΔGint-14 kcal/mol
Surface area35710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.637, 146.637, 92.934
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein ASFV DNA sliding clamp


Mass: 36821.891 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) African swine fever virus BA71V / Gene: E301R / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q65196
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.64 Å3/Da / Density % sol: 53.37 % / Mosaicity: 0.488 °
Crystal growTemperature: 289 K / Method: evaporation / pH: 8.5 / Details: Tris-HCl, PEG 3350, Ammonium Acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.29→50 Å / Num. obs: 33401 / % possible obs: 99.9 % / Redundancy: 8 % / Biso Wilson estimate: 43.21 Å2 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.043 / Rrim(I) all: 0.121 / Χ2: 1.117 / Net I/σ(I): 9.9 / Num. measured all: 267233
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.29-2.376.90.70733590.9080.2730.760.98299.5
2.37-2.4780.632960.9330.220.6391.025100
2.47-2.588.30.52433620.9410.1920.5581.058100
2.58-2.728.10.36533310.9720.1360.391.084100
2.72-2.898.50.24533420.9840.0890.2611.143100
2.89-3.118.40.17533440.990.0640.1861.084100
3.11-3.428.10.12233300.9930.0460.1311.081100
3.42-3.928.20.09233480.9960.0350.0981.057100
3.92-4.937.90.07433450.9960.0280.0791.174100
4.93-507.70.08133440.9950.0310.0871.474100

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Processing

Software
NameVersionClassification
PHENIX1.9refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.292→22.854 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 28.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2288 1823 5.46 %
Rwork0.1811 31536 -
obs0.1837 33359 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 157.31 Å2 / Biso mean: 52.7489 Å2 / Biso min: 28.63 Å2
Refinement stepCycle: final / Resolution: 2.292→22.854 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4481 0 0 125 4606
Biso mean---53.52 -
Num. residues----554
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084577
X-RAY DIFFRACTIONf_angle_d1.0786192
X-RAY DIFFRACTIONf_chiral_restr0.044711
X-RAY DIFFRACTIONf_plane_restr0.005778
X-RAY DIFFRACTIONf_dihedral_angle_d14.9961686
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2922-2.35410.30171240.2421239798
2.3541-2.42330.28941090.23612455100
2.4233-2.50150.29231480.23752449100
2.5015-2.59070.3091580.24232397100
2.5907-2.69430.29821780.22462401100
2.6943-2.81670.31781090.21112465100
2.8167-2.96490.27531170.20042407100
2.9649-3.15030.23921470.20832437100
3.1503-3.39280.22971590.19712420100
3.3928-3.73290.23151280.16952445100
3.7329-4.270.21841330.16042433100
4.27-5.36820.16171490.13992429100
5.3682-22.8540.21861640.17062401100

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