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- PDB-5yra: Crystal Structure of Cypovirus Polyhedra R13A/S193C/A194C Mutant -

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Basic information

Entry
Database: PDB / ID: 5yra
TitleCrystal Structure of Cypovirus Polyhedra R13A/S193C/A194C Mutant
ComponentsPolyhedrin
KeywordsVIRAL PROTEIN / In vivo protein crystal / polyhedra
Function / homologyCypovirus polyhedrin, Cypovirus 1 type / Cypovirus polyhedrin protein / viral occlusion body / host cell cytoplasm / Polyhedrin
Function and homology information
Biological speciesBombyx mori cytoplasmic polyhedrosis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.79 Å
AuthorsNegishi, H. / Abe, S. / Yamashita, K. / Hirata, K. / Niwase, K. / Boudes, M. / Coulibaly, F. / Mori, H. / Ueno, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
JSPS26620130 Japan
JSPS15J11955 Japan
CitationJournal: Chem. Commun. (Camb.) / Year: 2018
Title: Supramolecular protein cages constructed from a crystalline protein matrix
Authors: Negishi, H. / Abe, S. / Yamashita, K. / Hirata, K. / Niwase, K. / Boudes, M. / Coulibaly, F. / Mori, H. / Ueno, T.
History
DepositionNov 9, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)28,8898
Polymers28,4541
Non-polymers4347
Water1,72996
1
A: Polyhedrin
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)346,66896
Polymers341,45412
Non-polymers5,21484
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation12_555-y,-z,x1
Buried area51790 Å2
ΔGint-256 kcal/mol
Surface area120920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.700, 103.700, 103.700
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 / C-polyhedrin


Mass: 28454.484 Da / Num. of mol.: 1 / Mutation: R13A,S193C,A194C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bombyx mori cytoplasmic polyhedrosis virus
Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P11041
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 1

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Sample preparation

CrystalDensity Matthews: 1.63 Å3/Da / Density % sol: 24.68 %
Crystal growTemperature: 300 K / Method: in cell
Details: In vivo crystallization in the cytoplasm of the cell, temperature 300 K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.79→42.34 Å / Num. obs: 15866 / % possible obs: 100 % / Redundancy: 21.1 % / Net I/σ(I): 6.51

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementResolution: 1.79→42.34 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.773 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.147 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21784 1748 9.9 %RANDOM
Rwork0.15839 ---
obs0.16404 15866 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 17.521 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.79→42.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1965 0 28 96 2089
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0192057
X-RAY DIFFRACTIONr_bond_other_d0.0020.021866
X-RAY DIFFRACTIONr_angle_refined_deg1.7541.9282777
X-RAY DIFFRACTIONr_angle_other_deg1.02434272
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6115244
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.47823.739115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.98915326
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7781515
X-RAY DIFFRACTIONr_chiral_restr0.1140.2277
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022396
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02541
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3421.556967
X-RAY DIFFRACTIONr_mcbond_other1.3411.555966
X-RAY DIFFRACTIONr_mcangle_it2.0432.3241208
X-RAY DIFFRACTIONr_mcangle_other2.0432.3251209
X-RAY DIFFRACTIONr_scbond_it2.0851.881089
X-RAY DIFFRACTIONr_scbond_other2.0811.881089
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2812.71568
X-RAY DIFFRACTIONr_long_range_B_refined4.65913.2092354
X-RAY DIFFRACTIONr_long_range_B_other4.59313.1492338
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.791→1.837 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 127 -
Rwork0.306 1148 -
obs--100 %

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