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- PDB-5a96: Crystal structure of Lymantria dispar CPV14 polyhedra -

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Basic information

Entry
Database: PDB / ID: 5a96
TitleCrystal structure of Lymantria dispar CPV14 polyhedra
ComponentsPOLYHEDRIN
KeywordsVIRAL PROTEIN / INSECT VIRUS OCCLUSION BODY / MICROCRYSTAL
Function / homologyCypovirus polyhedrin / Cypovirus polyhedrin / GTP binding / GUANOSINE-5'-TRIPHOSPHATE / Polyhedrin
Function and homology information
Biological speciesLYMANTRIA DISPAR CYPOVIRUS 14
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.914 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 1.2Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / 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 / _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)29,2472
Polymers28,7231
Non-polymers5231
Water2,792155
1
A: POLYHEDRIN
hetero molecules

A: POLYHEDRIN
hetero molecules

A: POLYHEDRIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,7406
Polymers86,1703
Non-polymers1,5703
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation5_555z,x,y1
Buried area11530 Å2
ΔGint-47 kcal/mol
Surface area36140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.600, 102.600, 102.600
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: 28723.441 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: DISULFIDE BOND BETWEEN A 68 AND A 97 / Source: (gene. exp.) LYMANTRIA DISPAR CYPOVIRUS 14 / Cell line (production host): SF9 / 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 / Comment: GTP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 20

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Sample preparation

CrystalDensity Matthews: 1.6 Å3/Da / Density % sol: 22 % / 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 / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.91→72.5 Å / Num. obs: 12952 / % possible obs: 92.3 % / Observed criterion σ(I): 1 / Redundancy: 7.9 % / Biso Wilson estimate: 10.86 Å2 / Rmerge(I) obs: 0.2 / Net I/σ(I): 8.4
Reflection shellResolution: 1.91→2.02 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 1.8 / % possible all: 52.1

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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: 1.914→32.445 Å / SU ML: 0.15 / σ(F): 1.36 / Phase error: 18.19 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.194 831 7 %
Rwork0.1325 --
obs0.1369 11855 84.57 %
Solvent computationShrinkage radii: 0.29 Å / VDW probe radii: 0.5 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.426 Å2 / ksol: 0.462 e/Å3
Displacement parametersBiso mean: 13 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0 Å2
2--0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.914→32.445 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2022 0 32 155 2209
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082111
X-RAY DIFFRACTIONf_angle_d1.2252871
X-RAY DIFFRACTIONf_dihedral_angle_d15.776772
X-RAY DIFFRACTIONf_chiral_restr0.074299
X-RAY DIFFRACTIONf_plane_restr0.005369
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9145-2.03440.2524440.196587X-RAY DIFFRACTION27
2.0344-2.19150.25981240.1671774X-RAY DIFFRACTION82
2.1915-2.4120.22591650.14122103X-RAY DIFFRACTION98
2.412-2.76080.21161690.13392151X-RAY DIFFRACTION100
2.7608-3.47770.17561660.12072159X-RAY DIFFRACTION100
3.4777-32.44960.15341630.11752250X-RAY DIFFRACTION100

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