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- PDB-2wuy: the crystal structure of wild-type baculovirus polyhedra -

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Basic information

Entry
Database: PDB / ID: 2wuy
Titlethe crystal structure of wild-type baculovirus polyhedra
ComponentsPOLYHEDRIN
KeywordsVIRAL PROTEIN / MICROCRYSTALS / POLYHEDRA / VIRUS / VIRAL OCCLUSION BODY / VIRAL CAPSID
Function / homologyPolyhedrin / Polyhedrin / host cell nuclear matrix / viral occlusion body / structural molecule activity / identical protein binding / Polyhedrin
Function and homology information
Biological speciesAUTOGRAPHA CALIFORNICA NUCLEAR POLYHEDROSIS VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.09 Å
AuthorsJi, X. / Sutton, G. / Evans, G. / Axford, D. / Owen, R. / Stuart, D.I.
CitationJournal: Embo J. / Year: 2010
Title: How Baculovirus Polyhedra Fit Square Pegs Into Round Holes to Robustly Package Viruses.
Authors: Ji, X. / Sutton, G. / Evans, G. / Axford, D. / Owen, R. / Stuart, D.I.
History
DepositionOct 10, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 15, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: POLYHEDRIN


Theoretical massNumber of molelcules
Total (without water)28,6791
Polymers28,6791
Non-polymers00
Water00
1
A: POLYHEDRIN
x 12


Theoretical massNumber of molelcules
Total (without water)344,14512
Polymers344,14512
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation7_665-z+1,-x+1,y1
crystal symmetry operation10_656-y+1,z,-x+11
crystal symmetry operation5_555z,x,y1
crystal symmetry operation12_665-y+1,-z+1,x1
crystal symmetry operation11_566y,-z+1,-x+11
crystal symmetry operation4_566x,-y+1,-z+11
crystal symmetry operation8_656-z+1,x,-y+11
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation9_555y,z,x1
crystal symmetry operation6_566z,-x+1,-y+11
Buried area52580 Å2
ΔGint-291.5 kcal/mol
Surface area138280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.562, 101.562, 101.562
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein POLYHEDRIN


Mass: 28678.725 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AUTOGRAPHA CALIFORNICA NUCLEAR POLYHEDROSIS VIRUS
Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P04871

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 7

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Sample preparation

CrystalDensity Matthews: 1.52 Å3/Da / Density % sol: 20 % / Description: NONE
Crystal growpH: 7.5 / Details: pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9778
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 13, 2009 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 3329 / % possible obs: 99.6 % / Observed criterion σ(I): -1.5 / Redundancy: 6.8 % / Biso Wilson estimate: 51.05 Å2 / Rmerge(I) obs: 0.38 / Net I/σ(I): 4.4
Reflection shellResolution: 3→3.11 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 1.4 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.9.2refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WUX

2wux


Resolution: 3.09→41.46 Å / Cor.coef. Fo:Fc: 0.8823 / Cor.coef. Fo:Fc free: 0.829 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2378 144 4.3 %RANDOM
Rwork0.2046 ---
obs0.206 3314 99.6 %-
Displacement parametersBiso mean: 28.76 Å2
Refinement stepCycle: LAST / Resolution: 3.09→41.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1723 0 0 0 1723
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0071771HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.942404HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d601SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes47HARMONIC2
X-RAY DIFFRACTIONt_gen_planes248HARMONIC5
X-RAY DIFFRACTIONt_it1771HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.8
X-RAY DIFFRACTIONt_other_torsion17.26
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion221SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2173SEMIHARMONIC4
LS refinement shellResolution: 3.09→3.45 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2162 39 4.17 %
Rwork0.2289 897 -
all0.2284 936 -

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