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- PDB-7wlh: The crystal structure of African swine fever virus I215L -

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Basic information

Entry
Database: PDB / ID: 7wlh
TitleThe crystal structure of African swine fever virus I215L
ComponentsE2 ubiquitin-conjugating enzyme
KeywordsTRANSFERASE / ASFV / I215L / VIRAL PROTEIN
Function / homology
Function and homology information


E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein polyubiquitination / ubiquitin-dependent protein catabolic process / host cell cytoplasm / host cell nucleus / cytoplasm
Similarity search - Function
: / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like
Similarity search - Domain/homology
Ubiquitin-conjugating enzyme E2
Similarity search - Component
Biological speciesAfrican swine fever virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.65 Å
AuthorsShen, Z. / Liang, R. / Yang, Y. / Peng, G.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32102652 China
CitationJournal: To Be Published
Title: The crystal structure of African swine fever virus I215L
Authors: Shen, Z. / Liang, R. / Yang, Y. / Peng, G.
History
DepositionJan 13, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 19, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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
B: E2 ubiquitin-conjugating enzyme


Theoretical massNumber of molelcules
Total (without water)22,9331
Polymers22,9331
Non-polymers00
Water68538
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9220 Å2
Unit cell
Length a, b, c (Å)142.302, 142.302, 39.319
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-219-

HOH

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Components

#1: Protein E2 ubiquitin-conjugating enzyme / Ubiquitin carrier protein / Ubiquitin-conjugating enzyme E2 / Ubiquitin-protein ligase / pI215L


Mass: 22932.957 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) African swine fever virus
Gene: I215L CDS, I215L, ASFV-Georgia_4-165, ASFV_Kyiv_2016_131_00221
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A2X0TKQ7, E2 ubiquitin-conjugating enzyme
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 5.06 Å3/Da / Density % sol: 75.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Sodium Acetate: HCl (pH 4.6), and 2.8 M Sodium Formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 12713 / % possible obs: 94.5 % / Redundancy: 17.8 % / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.023 / Rrim(I) all: 0.101 / Χ2: 0.62 / Net I/σ(I): 5.6 / Num. measured all: 226540
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.65-2.7410.20.4368700.860.120.4540.47166.1
2.74-2.8511.80.42210800.9870.110.4370.45281.7
2.85-2.9814.80.42312900.990.1070.4380.47196.6
2.98-3.1418.80.42513280.9950.10.4360.47299.9
3.14-3.3420.60.32113460.9980.0730.330.523100
3.34-3.619.60.19413440.9980.0450.1990.618100
3.6-3.9620.60.12413440.9990.0280.1270.77100
3.96-4.5319.50.08513410.9990.020.0880.975100
4.53-5.7119.40.06813630.9990.0160.070.723100
5.71-5018.90.05814070.9990.0140.0590.48299.9

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.65→35.6 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.946 / SU B: 12.532 / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.236 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2407 631 5 %RANDOM
Rwork0.1964 ---
obs0.1986 12066 94.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 207.37 Å2 / Biso mean: 60 Å2 / Biso min: 60.43 Å2
Baniso -1Baniso -2Baniso -3
1-3.85 Å21.93 Å20 Å2
2--3.85 Å2-0 Å2
3----12.5 Å2
Refinement stepCycle: final / Resolution: 2.65→35.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1265 0 0 38 1303
Biso mean---98.76 -
Num. residues----156
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0131299
X-RAY DIFFRACTIONr_bond_other_d0.0010.0151216
X-RAY DIFFRACTIONr_angle_refined_deg1.8451.6571764
X-RAY DIFFRACTIONr_angle_other_deg1.1881.5772832
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.0595154
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.89423.23165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.01815216
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.461156
X-RAY DIFFRACTIONr_chiral_restr0.0750.2170
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021423
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02273
LS refinement shellResolution: 2.652→2.721 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.428 21 -
Rwork0.414 601 -
all-622 -
obs--63.47 %

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