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- PDB-5a9b: Crystal structure of Bombyx mori CPV1 polyhedra base domain delet... -

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Basic information

Entry
Database: PDB / ID: 5a9b
TitleCrystal structure of Bombyx mori CPV1 polyhedra base domain deleted mutant
ComponentsPOLYHEDRIN
KeywordsVIRAL PROTEIN / INSECT VIRUS OCCLUSION BODY / MICROCRYSTAL
Function / homologyCypovirus polyhedrin, Cypovirus 1 type / Cypovirus polyhedrin protein / viral occlusion body / host cell cytoplasm / Polyhedrin
Function and homology information
Biological speciesBOMBYX MORI CYPOVIRUS 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.883 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 1.2Jan 10, 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)24,7541
Polymers24,7541
Non-polymers00
Water1,820101
1
A: POLYHEDRIN

A: POLYHEDRIN

A: POLYHEDRIN


Theoretical massNumber of molelcules
Total (without water)74,2613
Polymers74,2613
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation5_555z,x,y1
Buried area8310 Å2
ΔGint-48.2 kcal/mol
Surface area29530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.860, 103.860, 103.860
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-2034-

HOH

21A-2066-

HOH

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Components

#1: Protein POLYHEDRIN /


Mass: 24753.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BOMBYX MORI CYPOVIRUS 1 / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P11041
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 13

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Sample preparation

CrystalDensity Matthews: 1.9 Å3/Da / Density % sol: 35 % / 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: 1.88→42.4 Å / Num. obs: 15023 / % possible obs: 98.8 % / Observed criterion σ(I): 1 / Redundancy: 4.3 % / Biso Wilson estimate: 25.4 Å2 / Rmerge(I) obs: 0.23 / Net I/σ(I): 4.8
Reflection shellResolution: 1.88→1.93 Å / Redundancy: 4 % / Mean I/σ(I) obs: 1 / % possible all: 98.6

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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

2oh6


Resolution: 1.883→42.401 Å / SU ML: 0.59 / σ(F): 1.34 / Phase error: 25.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2511 758 5.1 %
Rwork0.1885 --
obs0.1916 15016 98.42 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.847 Å2 / ksol: 0.413 e/Å3
Displacement parametersBiso mean: 36 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.883→42.401 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1683 0 0 101 1784
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031731
X-RAY DIFFRACTIONf_angle_d0.792349
X-RAY DIFFRACTIONf_dihedral_angle_d13.697630
X-RAY DIFFRACTIONf_chiral_restr0.058244
X-RAY DIFFRACTIONf_plane_restr0.002306
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8831-2.02850.36651540.27772811X-RAY DIFFRACTION98
2.0285-2.23260.31641480.22972835X-RAY DIFFRACTION99
2.2326-2.55560.28821530.20572823X-RAY DIFFRACTION98
2.5556-3.21960.26331530.17322859X-RAY DIFFRACTION99
3.2196-42.41140.19991500.16572930X-RAY DIFFRACTION98

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