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- PDB-5a8v: Crystal structure of Orgyia pseudotsugata CPV5 polyhedra with SeM... -

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Basic information

Entry
Database: PDB / ID: 5a8v
TitleCrystal structure of Orgyia pseudotsugata CPV5 polyhedra with SeMet substitution
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 / SIRAS / Resolution: 2.074 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

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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)28,7172
Polymers28,6771
Non-polymers401
Water2,018112
1
A: POLYHEDRIN
hetero molecules

A: POLYHEDRIN
hetero molecules

A: POLYHEDRIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,1516
Polymers86,0303
Non-polymers1203
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation5_555z,x,y1
Buried area11320 Å2
ΔGint-62 kcal/mol
Surface area32990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.054, 102.054, 102.054
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-1254-

CA

21A-2099-

HOH

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Components

#1: Protein POLYHEDRIN / / C-POLYHEDRIN


Mass: 28676.822 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: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 128

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Sample preparation

CrystalDensity Matthews: 1.5 Å3/Da / Density % sol: 21 % / 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: 2.07→72.2 Å / Num. obs: 10902 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 64.1 % / Biso Wilson estimate: 15.03 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 7.5
Reflection shellResolution: 2.07→2.14 Å / Redundancy: 26.1 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 1.9 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
xia2data reduction
xia2data scaling
SHARPphasing
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 2.074→36.082 Å / SU ML: 0.23 / σ(F): 1.3 / Phase error: 21.12 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2279 521 4.8 %
Rwork0.1689 --
obs0.1718 10889 99.91 %
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.987 Å2 / ksol: 0.475 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.074→36.082 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2002 0 1 112 2115
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062084
X-RAY DIFFRACTIONf_angle_d1.0152829
X-RAY DIFFRACTIONf_dihedral_angle_d18.131759
X-RAY DIFFRACTIONf_chiral_restr0.069283
X-RAY DIFFRACTIONf_plane_restr0.003375
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0737-2.28230.29571390.22492548X-RAY DIFFRACTION100
2.2823-2.61250.24871310.17722574X-RAY DIFFRACTION100
2.6125-3.29110.23271230.15062590X-RAY DIFFRACTION100
3.2911-36.0870.18661280.15432656X-RAY DIFFRACTION100

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