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- PDB-5a8u: Crystal structure of Orgyia pseudotsugata CPV5 polyhedra -

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Basic information

Entry
Database: PDB / ID: 5a8u
TitleCrystal structure of Orgyia pseudotsugata CPV5 polyhedra
ComponentsPOLYHEDRIN
KeywordsVIRAL PROTEIN / INSECT VIRUS OCCLUSION BODY / MICROCRYSTAL
Function / homologyviral occlusion body / Polyhedrin
Function and homology information
Biological speciesORGYIA PSEUDOTSUGATA CYPOVIRUS 5
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.609 Å
AuthorsJi, X. / Axford, D. / Owen, R. / Evans, G. / Ginn, H.M. / Sutton, G. / Stuart, D.I.
CitationJournal: J.Struct.Biol. / Year: 2015
Title: Polyhedra Structures and the Evolution of the Insect Viruses.
Authors: Ji, X. / Axford, D. / Owen, R. / Evans, G. / Ginn, H.M. / Sutton, G. / Stuart, D.I.
History
DepositionJul 17, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Database references
Revision 1.2Oct 23, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: pdbx_database_status / struct_conn / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Jan 10, 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
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)28,3491
Polymers28,3491
Non-polymers00
Water2,990166
1
A: POLYHEDRIN

A: POLYHEDRIN

A: POLYHEDRIN


Theoretical massNumber of molelcules
Total (without water)85,0463
Polymers85,0463
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation5_555z,x,y1
Buried area11240 Å2
ΔGint-64.4 kcal/mol
Surface area32800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.320, 102.320, 102.320
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-2071-

HOH

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Components

#1: Protein POLYHEDRIN / C-POLYHEDRIN


Mass: 28348.557 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ORGYIA PSEUDOTSUGATA CYPOVIRUS 5 / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P36701
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 26

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Sample preparation

CrystalDensity Matthews: 1.6 Å3/Da / Density % sol: 22 % / 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: 0.979
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.61→51.2 Å / Num. obs: 23283 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 14.8 % / Biso Wilson estimate: 8.2 Å2 / Rmerge(I) obs: 0.34 / Net I/σ(I): 7
Reflection shellResolution: 1.61→1.65 Å / Redundancy: 10.7 % / Mean I/σ(I) obs: 1.4 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
xia2data reduction
xia2data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5A8V

5a8v


Resolution: 1.609→51.16 Å / SU ML: 0.3 / σ(F): 1.34 / Phase error: 18.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1967 1197 5.1 %
Rwork0.159 --
obs0.161 23282 99.97 %
Solvent computationShrinkage radii: 0.49 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.551 Å2 / ksol: 0.431 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.609→51.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2002 0 0 166 2168
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082054
X-RAY DIFFRACTIONf_angle_d1.192782
X-RAY DIFFRACTIONf_dihedral_angle_d12.557745
X-RAY DIFFRACTIONf_chiral_restr0.086279
X-RAY DIFFRACTIONf_plane_restr0.004373
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6086-1.6730.27791260.23592450X-RAY DIFFRACTION100
1.673-1.74920.27251310.21252437X-RAY DIFFRACTION100
1.7492-1.84140.2381160.19642426X-RAY DIFFRACTION100
1.8414-1.95670.22931310.16762437X-RAY DIFFRACTION100
1.9567-2.10780.21331330.15342432X-RAY DIFFRACTION100
2.1078-2.320.18581410.14512452X-RAY DIFFRACTION100
2.32-2.65560.19851460.13652430X-RAY DIFFRACTION100
2.6556-3.34570.14731290.14122474X-RAY DIFFRACTION100
3.3457-51.18590.17451440.14882547X-RAY DIFFRACTION100

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