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- PDB-5cdd: Crystal Structure of Israel acute Paralysis Virus Pentamer -

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Basic information

Entry
Database: PDB / ID: 5cdd
TitleCrystal Structure of Israel acute Paralysis Virus Pentamer
Components
  • Structural polyprotein, VP1
  • Structural polyprotein, VP2
  • Structural polyprotein, VP3
KeywordsVIRUS / Pentamer / capsid / honeybee virus / pathogen
Function / homology
Function and homology information


structural molecule activity
Similarity search - Function
Capsid protein VP4, dicistrovirus / Cricket paralysis virus, VP4 / Dicistrovirus, capsid-polyprotein, C-terminal / CRPV capsid protein like / Picornavirus capsid / picornavirus capsid protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit
Similarity search - Domain/homology
Structural polyprotein / Structural polyprotein
Similarity search - Component
Biological speciesIsraeli acute paralysis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsMullapudi, E. / Plevka, P.
CitationJournal: J.Virol. / Year: 2016
Title: Virion Structure of Iflavirus Slow Bee Paralysis Virus at 2.6-Angstrom Resolution.
Authors: Kalynych, S. / Pridal, A. / Palkova, L. / Levdansky, Y. / de Miranda, J.R. / Plevka, P.
History
DepositionJul 3, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: Database references
Revision 1.2Aug 24, 2016Group: Database references
Revision 1.3May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Structural polyprotein, VP1
B: Structural polyprotein, VP3
C: Structural polyprotein, VP2


Theoretical massNumber of molelcules
Total (without water)79,6273
Polymers79,6273
Non-polymers00
Water23413
1
A: Structural polyprotein, VP1
B: Structural polyprotein, VP3
C: Structural polyprotein, VP2
x 10


Theoretical massNumber of molelcules
Total (without water)796,27030
Polymers796,27030
Non-polymers00
Water54030
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation9
2


  • Idetical with deposited unit
  • point asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit in distinct coordinate
  • point asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
Unit cell
Length a, b, c (Å)112.177, 274.248, 288.309
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
SymmetryPoint symmetry: (Schoenflies symbol: D5 (2x5 fold dihedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(-0.999996, -0.002302, 0.001795), (-0.002276, 0.999895, 0.014288), (-0.001827, 0.014284, -0.999896)0.51308, 0.23527, -44.55749
3generate(-0.999804, 0.014332, 0.013667), (0.017286, 0.294889, 0.955375), (0.009662, 0.955424, -0.295078)0.6795, 21.00632, -28.46054
4generate(0.999793, -0.016922, -0.011294), (0.016017, 0.31243, 0.949806), (-0.012544, -0.94979, 0.312636)-0.17733, 20.82702, -15.87189
5generate(0.999847, 0.013551, -0.01108), (-0.0147, 0.306336, -0.95181), (-0.009503, 0.951827, 0.306488)-0.20949, -21.4437, -15.12339
6generate(-0.999776, -0.016671, 0.013057), (-0.017743, 0.322893, -0.946269), (0.011559, -0.946289, -0.323117)0.70902, -21.41007, -29.92929
7generate(-0.999555, 0.006623, 0.029099), (0.011319, -0.81808, 0.574992), (0.027614, 0.575066, 0.817641)1.05069, 12.04954, -3.88384
8generate(0.999605, -0.00986, -0.026302), (0.007539, -0.807835, 0.58936), (-0.027059, -0.589326, -0.807442)-0.44777, 12.29299, -40.58977
9generate(-0.999603, -0.009822, 0.026425), (-0.007981, -0.800403, -0.59941), (0.027039, -0.599382, 0.800006)0.96559, -13.96919, -4.84497
10generate(0.999583, 0.009388, -0.027298), (-0.008465, -0.808733, -0.588116), (-0.027598, 0.588102, -0.808316)-0.65129, -13.8441, -40.2117

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Components

#1: Protein Structural polyprotein, VP1


Mass: 23881.695 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Israeli acute paralysis virus / References: UniProt: B3TZF1
#2: Protein Structural polyprotein, VP3


Mass: 33353.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Israeli acute paralysis virus / References: UniProt: D1FK67
#3: Protein Structural polyprotein, VP2


Mass: 22391.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Israeli acute paralysis virus / References: UniProt: D1FK67
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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

Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: 0.1M HEPES pH 7.5, 20% (w/v) PEG 10,000, 8% Ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99999 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 2.7→70 Å / Num. obs: 240313 / % possible obs: 98.69 % / Redundancy: 4.2 % / Net I/σ(I): 2.67

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHASERphasing
CNSrefinement
PDB_EXTRACT3.15data extraction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→70 Å / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2513 11837 4.9 %
Rwork0.2443 228476 -
obs-240313 98.7 %
Solvent computationBsol: 20.0391 Å2
Displacement parametersBiso max: 104.08 Å2 / Biso mean: 42.0621 Å2 / Biso min: 7.21 Å2
Baniso -1Baniso -2Baniso -3
1-9.834 Å20 Å20 Å2
2---2.719 Å20 Å2
3----7.115 Å2
Refinement stepCycle: final / Resolution: 2.7→70 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5604 0 0 13 5617
Biso mean---32.94 -
Num. residues----709
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.2261.5
X-RAY DIFFRACTIONc_scbond_it1.6892
X-RAY DIFFRACTIONc_mcangle_it2.1912
X-RAY DIFFRACTIONc_scangle_it2.6712.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION4CNS_TOPPAR:ion.param
X-RAY DIFFRACTION5CNS_TOPPAR:carbohydrate.param

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