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- PDB-5yrd: Crystal Structure of Oxidized Cypovirus Polyhedra R13A/S193C/A194... -

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Basic information

Entry
Database: PDB / ID: 5yrd
TitleCrystal Structure of Oxidized Cypovirus Polyhedra R13A/S193C/A194C Mutant
ComponentsPolyhedrin
KeywordsVIRAL PROTEIN / In vivo protein crystal / polyhedra / disulfide bond
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 / MOLECULAR REPLACEMENT / Resolution: 1.85 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 1.2Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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)28,7656
Polymers28,4541
Non-polymers3105
Water1,982110
1
A: Polyhedrin
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)345,17872
Polymers341,45412
Non-polymers3,72460
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 area52530 Å2
ΔGint-279 kcal/mol
Surface area119780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.620, 103.620, 103.620
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.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 1

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Sample preparation

CrystalDensity Matthews: 1.63 Å3/Da / Density % sol: 24.5 %
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: 1.85→42.3 Å / Num. obs: 14365 / % possible obs: 99.9 % / Redundancy: 9 % / Net I/σ(I): 5.52

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→42.3 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.926 / SU B: 4.387 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.185 / ESU R Free: 0.163 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2218 1580 9.9 %RANDOM
Rwork0.16202 ---
obs0.1677 14365 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 17.49 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.85→42.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1965 0 20 110 2095
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0192043
X-RAY DIFFRACTIONr_bond_other_d0.0020.021844
X-RAY DIFFRACTIONr_angle_refined_deg1.6851.9262760
X-RAY DIFFRACTIONr_angle_other_deg1.03834223
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1735242
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.67723.86114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.33715323
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6591514
X-RAY DIFFRACTIONr_chiral_restr0.1070.2276
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022384
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02536
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_it1.211.576965
X-RAY DIFFRACTIONr_mcbond_other1.2091.576964
X-RAY DIFFRACTIONr_mcangle_it1.8262.3571205
X-RAY DIFFRACTIONr_mcangle_other1.8262.3581206
X-RAY DIFFRACTIONr_scbond_it1.8961.8571076
X-RAY DIFFRACTIONr_scbond_other1.8951.8571076
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9662.6841555
X-RAY DIFFRACTIONr_long_range_B_refined4.32613.3642346
X-RAY DIFFRACTIONr_long_range_B_other4.27813.2982328
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 116 -
Rwork0.286 1045 -
obs--99.74 %

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