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- PDB-5a98: Crystal structure of Trichoplusia ni CPV15 polyhedra -

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Basic information

Entry
Database: PDB / ID: 5a98
TitleCrystal structure of Trichoplusia ni CPV15 polyhedra
ComponentsPOLYHEDRIN
KeywordsVIRAL PROTEIN / INSECT VIRUS OCCLUSION BODY / MICROCRYSTAL
Function / homologyATP binding / ADENOSINE-5'-TRIPHOSPHATE / Polyhedrin
Function and homology information
Biological speciesTRICHOPLUSIA NI CYPOVIRUS 15
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.816 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 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)30,0786
Polymers28,9901
Non-polymers1,0875
Water3,171176
1
A: POLYHEDRIN
hetero molecules

A: POLYHEDRIN
hetero molecules

A: POLYHEDRIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,23318
Polymers86,9713
Non-polymers3,26215
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation5_555z,x,y1
Buried area11970 Å2
ΔGint-58.5 kcal/mol
Surface area42500 Å2
MethodPQS
Unit cell
Length a, b, c (Å)102.890, 102.890, 102.890
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-2174-

HOH

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Components

#1: Protein POLYHEDRIN


Mass: 28990.496 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRICHOPLUSIA NI CYPOVIRUS 15 / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q9ELS6
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / 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: 40

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Sample preparation

CrystalDensity Matthews: 1.57 Å3/Da / Density % sol: 21.7 % / 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: 1.82→51.4 Å / Num. obs: 16418 / % possible obs: 99.7 % / Observed criterion σ(I): 1 / Redundancy: 7.8 % / Biso Wilson estimate: 17.11 Å2 / Rmerge(I) obs: 0.47 / Net I/σ(I): 4.2
Reflection shellResolution: 1.82→1.86 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 0.8 / % possible all: 97.9

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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: 1.816→42.005 Å / SU ML: 0.55 / σ(F): 1.33 / Phase error: 21.93 / Stereochemistry target values: MLHL / Details: RESIDUES 66-78 ARE DISORDERED.
RfactorNum. reflection% reflection
Rfree0.2199 830 5.1 %
Rwork0.1617 --
obs0.1646 16408 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.085 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 17.6 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.816→42.005 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1940 0 65 176 2181
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072071
X-RAY DIFFRACTIONf_angle_d1.2762813
X-RAY DIFFRACTIONf_dihedral_angle_d16.986782
X-RAY DIFFRACTIONf_chiral_restr0.078283
X-RAY DIFFRACTIONf_plane_restr0.006360
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.816-1.92980.37271530.2922467X-RAY DIFFRACTION97
1.9298-2.07880.30941420.21592604X-RAY DIFFRACTION100
2.0788-2.2880.25121420.17512574X-RAY DIFFRACTION100
2.288-2.6190.24241260.16162615X-RAY DIFFRACTION100
2.619-3.29950.1931320.14042621X-RAY DIFFRACTION100
3.2995-42.01590.15111350.12682697X-RAY DIFFRACTION100

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