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- PDB-3jw6: Crystal structure of AcMNPV baculovirus polyhedra -

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Basic information

Entry
Database: PDB / ID: 3jw6
TitleCrystal structure of AcMNPV baculovirus polyhedra
ComponentsPolyhedrin
KeywordsVIRAL PROTEIN / Jelly-roll / disulfide bond / domain swapping / Viral occlusion body
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 / MIR / Resolution: 2.3 Å
AuthorsCoulibaly, F. / Chiu, E. / Metcalf, P.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: The atomic structure of baculovirus polyhedra reveals the independent emergence of infectious crystals in DNA and RNA viruses
Authors: Coulibaly, F. / Chiu, E. / Gutmann, S. / Rajendran, C. / Haebel, P.W. / Ikeda, K. / Mori, H. / Ward, V.K. / Schulze-Briese, C. / Metcalf, P.
History
DepositionSep 17, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Jul 25, 2018Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / entity_src_nat / pdbx_struct_mod_residue / software / struct_ref_seq_dif
Item: _entity.src_method / _pdbx_struct_mod_residue.details / _struct_ref_seq_dif.details
Revision 1.4Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polyhedrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0802
Polymers29,0181
Non-polymers621
Water1,33374
1
A: Polyhedrin
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)348,96224
Polymers348,21812
Non-polymers74512
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_566z,-x+1,-y+11
crystal symmetry operation7_665-z+1,-x+1,y1
crystal symmetry operation8_656-z+1,x,-y+11
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_656-y+1,z,-x+11
crystal symmetry operation11_566y,-z+1,-x+11
crystal symmetry operation12_665-y+1,-z+1,x1
Buried area56170 Å2
ΔGint-266 kcal/mol
Surface area107520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.183, 103.183, 103.183
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-308-

HOH

21A-309-

HOH

DetailsPOLYHEDRA ARE VIRUS-CONTAINING CRYSTALS, WHICH REPRESENT THE MAIN INFECTIOUS FORM OF BACULOVIRUS. THE BIOLOGICAL ASSEMBLY IS THE WHOLE CRYSTAL. DODECAMERS OF THE POLYHEDRIN PROTEIN ARE PUTATIVE BUILDING BLOCKS OF THE CRYSTAL, WHICH ARE GENERATED BY THE SYMMETRY OPERATIONS.

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Components

#1: Protein Polyhedrin / Major occlusion protein


Mass: 29018.131 Da / Num. of mol.: 1 / Mutation: G25D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Autographa californica nuclear polyhedrosis virus
Description: Crystals were purified from Sf21 cells infected by the Autographa californica Multicapsid Nucleopolyhedrovirus (AcMNPV)
Cell: Sf21 / Gene: PH, P29, POLH / Cell line (production host): sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P04871
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 5

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Sample preparation

CrystalDensity Matthews: 1.579947 Å3/Da / Density % sol: 22.149273 % / Mosaicity: 0.477 °
Crystal growTemperature: 300 K / pH: 7
Details: Natural intracellular crystals were directly purified from Sf21 cells infected by the AcMNPV baculovirus, pH 7, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9789 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 17, 2007 / Details: MD2 microdiffractometer
RadiationMonochromator: SAGITALLY HORIZONTAL FOCUSSING SI(111) MERIDIONALLY VERTICAL FOCUSSING RH-COATED MIRROR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. all: 8281 / Num. obs: 8256 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 31.1 Å2 / Rmerge(I) obs: 0.149 / Χ2: 0.998 / Net I/σ(I): 6.2
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 3.8 / Num. unique all: 800 / Χ2: 0.963 / % possible all: 99.1

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Phasing

PhasingMethod: MIR

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
PDB_EXTRACT3.005data extraction
MAR345data collection
BUSTER-TNT2.8.0refinement
RefinementMethod to determine structure: MIR / Resolution: 2.3→18.84 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.918 / Occupancy max: 1 / Occupancy min: 0.5 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Residue ACys132 forms a disulfide bond with residue BCys132 of symmetry molecule 4566. By symmetry, this also implies that residue BCys132 forms a disulfide bond with residue ACys132 of symmetry molecule 4566.
RfactorNum. reflection% reflectionSelection details
Rfree0.214 811 9.84 %RANDOM
Rwork0.161 ---
all0.166 8240 --
obs0.166 8240 99.7 %-
Displacement parametersBiso max: 87.92 Å2 / Biso mean: 24.422 Å2 / Biso min: 7.2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.199 Å
Refinement stepCycle: LAST / Resolution: 2.3→18.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1577 0 4 74 1655
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.008
X-RAY DIFFRACTIONo_angle_deg1.04
X-RAY DIFFRACTIONo_dihedral_angle_d18.55
LS refinement shellResolution: 2.3→2.57 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.235 230 10 %
Rwork0.164 2069 -
all0.171 2299 -

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