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- PDB-5a8s: Crystal structure of Antheraea mylitta CPV4 polyhedra type 1 -

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Basic information

Entry
Database: PDB / ID: 5a8s
TitleCrystal structure of Antheraea mylitta CPV4 polyhedra type 1
ComponentsPOLYHEDRIN
KeywordsVIRAL PROTEIN / INSECT VIRUS OCCLUSION BODY / MICROCRYSTAL
Function / homologyCypovirus polyhedrin / Cypovirus polyhedrin / Polyhedrin
Function and homology information
Biological speciesANTHERAEA MYLITTA CYPOVIRUS 4
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.724 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 16, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Database references
Revision 2.0Oct 23, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / pdbx_database_status ...atom_site / pdbx_database_status / struct_conn / struct_ref_seq_dif
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 2.1Jan 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

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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)28,7751
Polymers28,7751
Non-polymers00
Water3,171176
1
A: POLYHEDRIN

A: POLYHEDRIN

A: POLYHEDRIN


Theoretical massNumber of molelcules
Total (without water)86,3253
Polymers86,3253
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation5_555z,x,y1
Buried area11230 Å2
ΔGint-52 kcal/mol
Surface area33380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.682, 101.682, 101.682
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-2031-

HOH

21A-2072-

HOH

31A-2176-

HOH

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Components

#1: Protein POLYHEDRIN /


Mass: 28775.158 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ANTHERAEA MYLITTA CYPOVIRUS 4 / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q67G25
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 18

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Sample preparation

CrystalDensity Matthews: 1.5 Å3/Da / Density % sol: 19 % / 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: 1.72→29.4 Å / Num. obs: 17233 / % possible obs: 92.7 % / Observed criterion σ(I): 1 / Redundancy: 11.4 % / Biso Wilson estimate: 11.4 Å2 / Rmerge(I) obs: 0.2 / Net I/σ(I): 9.7
Reflection shellResolution: 1.72→1.82 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 1.7 / % possible all: 59

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OH6 AND STRUCTURE OF CPV5 POLYHEDRIN

2oh6


Resolution: 1.724→29.353 Å / SU ML: 0.13 / σ(F): 0 / Phase error: 14.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1658 1728 10.03 %
Rwork0.1183 --
obs0.123 17227 92.54 %
Solvent computationShrinkage radii: 0.29 Å / VDW probe radii: 0.5 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.662 Å2 / ksol: 0.455 e/Å3
Displacement parametersBiso mean: 7.4 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.724→29.353 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2028 0 0 176 2204
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062074
X-RAY DIFFRACTIONf_angle_d1.0922821
X-RAY DIFFRACTIONf_dihedral_angle_d13.672758
X-RAY DIFFRACTIONf_chiral_restr0.073304
X-RAY DIFFRACTIONf_plane_restr0.006375
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7237-1.77440.3125650.2343589X-RAY DIFFRACTION42
1.7744-1.83160.2891230.20251132X-RAY DIFFRACTION82
1.8316-1.89710.23431370.18371233X-RAY DIFFRACTION90
1.8971-1.9730.24521470.15631327X-RAY DIFFRACTION96
1.973-2.06280.20811540.131395X-RAY DIFFRACTION100
2.0628-2.17150.15531570.10931376X-RAY DIFFRACTION100
2.1715-2.30750.15971570.10931395X-RAY DIFFRACTION100
2.3075-2.48560.17321520.10571396X-RAY DIFFRACTION100
2.4856-2.73560.17521590.10841389X-RAY DIFFRACTION100
2.7356-3.13110.13761540.09871396X-RAY DIFFRACTION100
3.1311-3.94330.12511570.09471413X-RAY DIFFRACTION100
3.9433-29.35730.12541660.10871458X-RAY DIFFRACTION100

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