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- PDB-6si6: N-terminal domain of Drosophila X virus VP3 -

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Basic information

Entry
Database: PDB / ID: 6si6
TitleN-terminal domain of Drosophila X virus VP3
ComponentsStructural polyprotein
KeywordsVIRAL PROTEIN / dsRNA binding protein
Function / homology
Function and homology information


T=13 icosahedral viral capsid / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / host cell cytoplasm / structural molecule activity / proteolysis / metal ion binding
Similarity search - Function
Birnavirus VP2 protein / Birnavirus VP3 protein / Birnavirus VP4 protease domain / Birnavirus VP2 protein / Birnavirus VP3 protein / Birnavirus VP4 protein / Birnavirus VP4 protease domain profile. / Viral coat protein subunit
Similarity search - Domain/homology
IMIDAZOLE / Structural polyprotein
Similarity search - Component
Biological speciesDrosophila x virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsFerrero, D.S. / Garriga, D. / Guerra, P. / Uson, I. / Verdaguer, N.
Funding support Spain, 2items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesBIO2017-83906-P Spain
Spanish Ministry of Science, Innovation, and UniversitiesMDM-2014-0435 Spain
CitationJournal: J.Virol. / Year: 2020
Title: Structure and dsRNA-binding activity of the Birnavirus Drosophila X Virus VP3 protein.
Authors: Ferrero, D.S. / Busnadiego, I. / Garriga, D. / Guerra, P. / Martin, M.T. / Kremer, L. / Uson, I. / Rodriguez, J.F. / Verdaguer, N.
History
DepositionAug 8, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2021Group: Database references / Category: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Structural polyprotein
B: Structural polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,8754
Polymers70,7142
Non-polymers1612
Water82946
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-26 kcal/mol
Surface area5440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.334, 45.334, 104.527
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21(chain B and (resid 35 through 80 or resid 83))

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA35 - 81
211(chain B and (resid 35 through 80 or resid 83))B0

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Components

#1: Protein Structural polyprotein / PP


Mass: 35356.797 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila x virus (isolate Chung/1996)
Strain: isolate Chung/1996 / Production host: Escherichia coli (E. coli)
References: UniProt: Q96724, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.46 Å3/Da / Density % sol: 49.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 12% PEG 4K, 200 mM ammonium sulphate and 100 mM sodium acetate pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97166 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97166 Å / Relative weight: 1
ReflectionResolution: 1.98→41.6 Å / Num. obs: 8128 / % possible obs: 99.94 % / Redundancy: 7.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.05459 / Rpim(I) all: 0.02 / Net I/σ(I): 23.01
Reflection shellResolution: 1.98→2.051 Å / Num. unique obs: 780 / CC1/2: 0.986

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Processing

Software
NameVersionClassification
PHENIXdev_3084refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6shw

6shw


Resolution: 1.98→41.591 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 22.4
RfactorNum. reflection% reflection
Rfree0.209 380 4.68 %
Rwork0.1741 --
obs0.1756 8128 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 136.62 Å2 / Biso mean: 46.0206 Å2 / Biso min: 20.97 Å2
Refinement stepCycle: final / Resolution: 1.98→41.591 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms762 0 24 46 832
Biso mean--72.18 51.42 -
Num. residues----98
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A442X-RAY DIFFRACTION7.806TORSIONAL
12B442X-RAY DIFFRACTION7.806TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.9801-2.26660.28351210.19782512
2.2666-2.85550.23981270.19652537
2.8555-41.590.18461320.16082699
Refinement TLS params.Method: refined / Origin x: -17.6976 Å / Origin y: -4.8716 Å / Origin z: 11.3976 Å
111213212223313233
T0.2481 Å2-0.0034 Å20.0102 Å2-0.1603 Å2-0.0217 Å2--0.2199 Å2
L4.9191 °2-0.9889 °20.8681 °2-6.419 °2-0.8655 °2--6.4223 °2
S-0.0094 Å °0.0002 Å °0.0894 Å °-0.082 Å °-0.0044 Å °-0.0781 Å °-0.0231 Å °-0.2669 Å °-0.0113 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA35 - 81
2X-RAY DIFFRACTION1allC1
3X-RAY DIFFRACTION1allC2
4X-RAY DIFFRACTION1allB33 - 83
5X-RAY DIFFRACTION1allS1 - 56

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