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- PDB-8qph: Crystal structure of Lymantria dispar CPV14 polyhedra 14 crystals -

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Basic information

Entry
Database: PDB / ID: 8qph
TitleCrystal structure of Lymantria dispar CPV14 polyhedra 14 crystals
ComponentsPolyhedrin
KeywordsVIRAL PROTEIN / Polyhedrin / GTP binding
Function / homologyCypovirus polyhedrin / Cypovirus polyhedrin / GTP binding / GUANOSINE-5'-TRIPHOSPHATE / Polyhedrin
Function and homology information
Biological speciesLymantria dispar (gypsy moth)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 Å
AuthorsTrincao, J. / Warren, A. / Crawshaw, A. / Sutton, G. / Stuart, D. / Evans, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: J.Synchrotron Radiat. / Year: 2024
Title: VMXm - A sub-micron focus macromolecular crystallography beamline at Diamond Light Source.
Authors: Warren, A.J. / Trincao, J. / Crawshaw, A.D. / Beale, E.V. / Duller, G. / Stallwood, A. / Lunnon, M. / Littlewood, R. / Prescott, A. / Foster, A. / Smith, N. / Rehm, G. / Gayadeen, S. / ...Authors: Warren, A.J. / Trincao, J. / Crawshaw, A.D. / Beale, E.V. / Duller, G. / Stallwood, A. / Lunnon, M. / Littlewood, R. / Prescott, A. / Foster, A. / Smith, N. / Rehm, G. / Gayadeen, S. / Bloomer, C. / Alianelli, L. / Laundy, D. / Sutter, J. / Cahill, L. / Evans, G.
#1: Journal: 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
DepositionOct 2, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _pdbx_entry_details.has_protein_modification
Revision 1.2Nov 20, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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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)29,2713
Polymers28,7231
Non-polymers5472
Water3,675204
1
A: Polyhedrin
hetero molecules
x 11
A: Polyhedrin
hetero molecules

A: Polyhedrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)380,52239
Polymers373,40513
Non-polymers7,11726
Water23413
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation12
MethodPQS
Unit cell
Length a, b, c (Å)103.189, 103.189, 103.189
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Space group name HallI223
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y,-z,x
#5: z,-x,-y
#6: -y,z,-x
#7: -z,-x,y
#8: -z,x,-y
#9: y,-z,-x
#10: x,-y,-z
#11: -x,y,-z
#12: -x,-y,z
#13: x+1/2,y+1/2,z+1/2
#14: z+1/2,x+1/2,y+1/2
#15: y+1/2,z+1/2,x+1/2
#16: -y+1/2,-z+1/2,x+1/2
#17: z+1/2,-x+1/2,-y+1/2
#18: -y+1/2,z+1/2,-x+1/2
#19: -z+1/2,-x+1/2,y+1/2
#20: -z+1/2,x+1/2,-y+1/2
#21: y+1/2,-z+1/2,-x+1/2
#22: x+1/2,-y+1/2,-z+1/2
#23: -x+1/2,y+1/2,-z+1/2
#24: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-593-

HOH

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Components

#1: Protein Polyhedrin


Mass: 28723.441 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lymantria dispar (gypsy moth) / Gene: pod / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q91IE3
#2: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.6 Å3/Da / Density % sol: 22 % / Description: Cubic
Crystal growTemperature: 300 K / Method: in cell / pH: 7.5 / Details: In vivo

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: VMXm / Wavelength: 0.5814 Å
DetectorType: DECTRIS EIGER2 X CdTe 9M / Detector: PIXEL / Date: Sep 29, 2021
RadiationMonochromator: Horizontal Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.5814 Å / Relative weight: 1
ReflectionResolution: 1.34→72.97 Å / Num. obs: 39736 / % possible obs: 96.6 % / Redundancy: 43.3 % / Biso Wilson estimate: 16.59 Å2 / CC1/2: 0.867 / Net I/σ(I): 9.4
Reflection shellResolution: 1.34→1.388 Å / Redundancy: 15.6 % / Num. unique obs: 4090 / CC1/2: 0.302 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
xia2.multiplexdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.34→72.97 Å / SU ML: 0.2022 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.0633
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1803 1984 5.01 %
Rwork0.1559 37633 -
obs0.1571 39617 96.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.42 Å2
Refinement stepCycle: LAST / Resolution: 1.34→72.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1966 0 33 204 2203
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00782078
X-RAY DIFFRACTIONf_angle_d1.14062832
X-RAY DIFFRACTIONf_chiral_restr0.0995296
X-RAY DIFFRACTIONf_plane_restr0.0082363
X-RAY DIFFRACTIONf_dihedral_angle_d15.1665756
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.34-1.370.38231440.35482696X-RAY DIFFRACTION98.24
1.37-1.410.34711460.33812751X-RAY DIFFRACTION99.59
1.41-1.450.31851460.31672769X-RAY DIFFRACTION99.86
1.45-1.50.33831470.2832753X-RAY DIFFRACTION100
1.5-1.550.22781410.24022765X-RAY DIFFRACTION99.97
1.55-1.610.22981460.19242770X-RAY DIFFRACTION100
1.62-1.690.22061440.18362749X-RAY DIFFRACTION100
1.69-1.780.21651500.16522791X-RAY DIFFRACTION99.97
1.78-1.890.19781130.182092X-RAY DIFFRACTION75.85
1.89-2.030.17861450.13992797X-RAY DIFFRACTION99.97
2.04-2.240.17561150.14622204X-RAY DIFFRACTION79.04
2.24-2.560.16351490.13192790X-RAY DIFFRACTION100
2.56-3.230.14591490.12712822X-RAY DIFFRACTION100
3.23-72.970.13531490.12172884X-RAY DIFFRACTION99.44

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