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- PDB-8i6g: Crystal structure of the African swine fever virus DNA sliding cl... -

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Basic information

Entry
Database: PDB / ID: 8i6g
TitleCrystal structure of the African swine fever virus DNA sliding clamp (native 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 / MOLECULAR REPLACEMENT / Resolution: 1.79 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 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)72,8932
Polymers72,8932
Non-polymers00
Water3,981221
1
A: ASFV DNA sliding clamp

A: ASFV DNA sliding clamp

A: ASFV DNA sliding clamp


Theoretical massNumber of molelcules
Total (without water)109,3403
Polymers109,3403
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 area5240 Å2
ΔGint-14 kcal/mol
Surface area35490 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)109,3403
Polymers109,3403
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-12 kcal/mol
Surface area35150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.767, 146.767, 94.491
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: 36446.734 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


Mass: 18.015 Da / Num. of mol.: 221 / 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: 2.69 Å3/Da / Density % sol: 54.22 % / Mosaicity: 0.496 °
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: Jan 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.79→50 Å / Num. obs: 69816 / % possible obs: 97.1 % / Redundancy: 4.8 % / Biso Wilson estimate: 33.66 Å2 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.022 / Rrim(I) all: 0.049 / Χ2: 0.977 / Net I/σ(I): 17.5 / Num. measured all: 332433
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.79-1.853.30.53659020.8050.3230.630.94381.7
1.85-1.933.70.40466340.9060.2270.4650.99992.2
1.93-2.024.50.27470110.9690.1410.3091.04297.8
2.02-2.1250.19971530.9850.0980.2221.05699.7
2.12-2.265.10.1471960.9920.0690.1561.024100
2.26-2.435.30.08872010.9970.0420.0980.999100
2.43-2.675.20.06571790.9970.0320.0730.952100
2.67-3.065.20.04771870.9980.0230.0530.916100
3.06-3.865.10.03872020.9990.0180.0420.858100
3.86-5050.03471510.9980.0170.0380.98499.3

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Processing

Software
NameVersionClassification
PHENIX1.9refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8I6H

8i6h


Resolution: 1.79→22.386 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.95 / Phase error: 30.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2302 3714 5.35 %
Rwork0.203 65729 -
obs0.2045 69443 97.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.54 Å2 / Biso mean: 42.7138 Å2 / Biso min: 23.76 Å2
Refinement stepCycle: final / Resolution: 1.79→22.386 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4452 0 0 222 4674
Biso mean---45.2 -
Num. residues----554
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074547
X-RAY DIFFRACTIONf_angle_d1.0366154
X-RAY DIFFRACTIONf_chiral_restr0.046710
X-RAY DIFFRACTIONf_plane_restr0.006772
X-RAY DIFFRACTIONf_dihedral_angle_d14.681666
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.79-1.81270.28791220.2997197179
1.8127-1.83650.29751140.2976206283
1.8365-1.86170.34881410.2879212786
1.8617-1.88820.32361270.2876230892
1.8882-1.91640.31071380.2797237194
1.9164-1.94630.32521210.2645238196
1.9463-1.97820.30661230.2515249598
1.9782-2.01230.30871420.2558247599
2.0123-2.04890.25731570.2479244799
2.0489-2.08830.28181650.25122449100
2.0883-2.13090.26881200.23292552100
2.1309-2.17720.28581280.23952518100
2.1772-2.22780.24541180.23742504100
2.2278-2.28340.2761270.23762551100
2.2834-2.34510.25881250.22012536100
2.3451-2.4140.21381190.23152516100
2.414-2.49190.26311360.23232538100
2.4919-2.58080.27411610.24282499100
2.5808-2.6840.2931870.24042449100
2.684-2.80590.28191370.22822485100
2.8059-2.95350.2721110.22732546100
2.9535-3.13810.27641390.22622509100
3.1381-3.37960.20641560.2082499100
3.3796-3.71830.21031450.1822486100
3.7183-4.25320.18681410.17222517100
4.2532-5.34650.16421460.14822498100
5.3465-22.3860.21471680.1735244098

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