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- PDB-5a9c: Crystal structure of Antheraea mylitta CPV4 polyhedra base domain... -

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Basic information

Entry
Database: PDB / ID: 5a9c
TitleCrystal structure of Antheraea mylitta CPV4 polyhedra base domain deleted mutant
ComponentsPOLYHEDRIN
KeywordsVIRAL PROTEIN / INSECT VIRUS OCCLUSION BODY / MICROCRYSTAL
Function / homologyCypovirus polyhedrin / Cypovirus polyhedrin / membrane / Polyhedrin / Polyhedrin
Function and homology information
Biological speciesANTHERAEA MYLITTA CYPOVIRUS 4
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 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 21, 2015Group: Database references
Revision 1.2May 1, 2024Group: 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)24,8191
Polymers24,8191
Non-polymers00
Water2,450136
1
A: POLYHEDRIN

A: POLYHEDRIN

A: POLYHEDRIN


Theoretical massNumber of molelcules
Total (without water)74,4573
Polymers74,4573
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation5_555z,x,y1
Buried area7360 Å2
ΔGint-37.9 kcal/mol
Surface area28020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.330, 104.330, 104.330
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: 24818.990 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: Q67G23, UniProt: Q67G25*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 21

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Sample preparation

CrystalDensity Matthews: 1.9 Å3/Da / Density % sol: 35.7 % / 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: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.71→33 Å / Num. obs: 19985 / % possible obs: 97.3 % / Observed criterion σ(I): 1 / Redundancy: 4.4 % / Biso Wilson estimate: 15.8 Å2 / Rmerge(I) obs: 0.19 / Net I/σ(I): 5
Reflection shellResolution: 1.71→1.75 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 0.6 / % possible all: 88.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CPV4 POLYHEDRA TYPE 2 STRUCTURE

Resolution: 1.71→27.883 Å / SU ML: 0.46 / σ(F): 1.34 / Phase error: 21.7 / Stereochemistry target values: ML / Details: RESIDUES 1-12, 189-192 ARE DISORDERED.
RfactorNum. reflection% reflection
Rfree0.2158 1018 5.1 %
Rwork0.1853 --
obs0.1869 19908 96.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.265 Å2 / ksol: 0.401 e/Å3
Displacement parametersBiso mean: 27.6 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.71→27.883 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1628 0 0 136 1764
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031664
X-RAY DIFFRACTIONf_angle_d0.7352261
X-RAY DIFFRACTIONf_dihedral_angle_d12.038606
X-RAY DIFFRACTIONf_chiral_restr0.055245
X-RAY DIFFRACTIONf_plane_restr0.004298
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7096-1.79980.36141440.33842467X-RAY DIFFRACTION89
1.7998-1.91250.32421390.27912650X-RAY DIFFRACTION96
1.9125-2.06010.25091370.21572734X-RAY DIFFRACTION99
2.0601-2.26740.22581490.18542729X-RAY DIFFRACTION98
2.2674-2.59520.22551470.17612729X-RAY DIFFRACTION98
2.5952-3.26890.18571560.15582762X-RAY DIFFRACTION99
3.2689-27.88710.18691460.16842819X-RAY DIFFRACTION97

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