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- PDB-9eqn: N-terminal domain of Infectious Bursal Disease Virus (IBDV) VP3 -

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Basic information

Entry
Database: PDB / ID: 9eqn
TitleN-terminal domain of Infectious Bursal Disease Virus (IBDV) VP3
ComponentsStructural polyprotein
KeywordsVIRAL PROTEIN / dsRNA binding protein / Birnavirus / IBDV
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 / identical protein binding / metal ion binding
Similarity search - Function
Birnavirus VP3, domain 2 / Birnavirus VP3, domain 1 / 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
ETHANOL / Structural polyprotein
Similarity search - Component
Biological speciesInfectious bursal disease virus (Gumboro virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.46 Å
AuthorsFerrero, D.S. / Verdaguer, N.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPID2020-117976GB-I00 Spain
CitationJournal: To Be Published
Title: Structure of the amino terminal domain of the Birnaviral multifunctional VP3 protein and its unexplored critical role
Authors: Ferrero, D.S. / Verdaguer, N.
History
DepositionMar 22, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)33,2756
Polymers33,1374
Non-polymers1382
Water4,035224
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-46 kcal/mol
Surface area7530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.670, 55.761, 52.894
Angle α, β, γ (deg.)90.00, 110.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Structural polyprotein / PP


Mass: 8284.283 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Infectious bursal disease virus (Gumboro virus)
Plasmid: pREST-C / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P61825
#2: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.19 Å3/Da / Density % sol: 43.89 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 1.5M NaCl, 0.1M Sodium Acetate pH4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Apr 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.46→45.7 Å / Num. obs: 43928 / % possible obs: 94.94 % / Redundancy: 6.7 % / Biso Wilson estimate: 15.13 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.08931 / Rpim(I) all: 0.03561 / Rrim(I) all: 0.09636 / Net I/σ(I): 13.19
Reflection shellResolution: 1.46→1.49 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.8215 / Mean I/σ(I) obs: 1.46 / Num. unique obs: 1925 / CC1/2: 0.517 / Rpim(I) all: 0.4776 / Rrim(I) all: 0.9567 / % possible all: 62.72

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Processing

Software
NameVersionClassification
PHENIX(dev_4788: ???)refinement
XDSdata reduction
Aimlessdata scaling
Arcimboldophasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.46→45.7 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2084 2162 4.92 %Random selection
Rwork0.1747 ---
obs0.1764 43928 94.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.46→45.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2155 0 0 224 2379
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009
X-RAY DIFFRACTIONf_angle_d0.993
X-RAY DIFFRACTIONf_dihedral_angle_d13.67804
X-RAY DIFFRACTIONf_chiral_restr0.067332
X-RAY DIFFRACTIONf_plane_restr0.007410
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.46-1.490.28711040.23591821X-RAY DIFFRACTION63
1.49-1.530.26411070.21522196X-RAY DIFFRACTION75
1.53-1.570.2621460.20622615X-RAY DIFFRACTION89
1.57-1.620.2511220.19382863X-RAY DIFFRACTION98
1.62-1.670.18461390.17452901X-RAY DIFFRACTION99
1.67-1.730.24221420.16032921X-RAY DIFFRACTION100
1.73-1.80.22781560.16432908X-RAY DIFFRACTION100
1.8-1.880.20611420.16112944X-RAY DIFFRACTION100
1.88-1.980.22391530.17122905X-RAY DIFFRACTION100
1.98-2.110.24061700.16462919X-RAY DIFFRACTION100
2.11-2.270.17691650.15662910X-RAY DIFFRACTION100
2.27-2.50.16711860.15212911X-RAY DIFFRACTION100
2.5-2.860.19941490.16842957X-RAY DIFFRACTION100
2.86-3.60.19671300.17452973X-RAY DIFFRACTION100
3.6-45.70.21981510.19423022X-RAY DIFFRACTION100

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