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- PDB-7wyr: Crystal structure of Cypovirus Polyhedra mutant fused with CLN025 -

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Basic information

Entry
Database: PDB / ID: 7wyr
TitleCrystal structure of Cypovirus Polyhedra mutant fused with CLN025
ComponentsPolyhedrin fused with CLN025
KeywordsVIRAL PROTEIN
Function / homologyCypovirus polyhedrin, Cypovirus 1 type / Cypovirus polyhedrin protein / viral occlusion body / host cell cytoplasm / Polyhedrin
Function and homology information
Biological speciesBombyx mori cypovirus 1
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsKojima, M. / Abe, S. / Hirata, K. / Yamashita, K. / Ueno, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Biomater Sci / Year: 2023
Title: Engineering of an in-cell protein crystal for fastening a metastable conformation of a target miniprotein.
Authors: Kojima, M. / Abe, S. / Furuta, T. / Tran, D.P. / Hirata, K. / Yamashita, K. / Hishikawa, Y. / Kitao, A. / Ueno, T.
History
DepositionFeb 16, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polyhedrin fused with CLN025
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2144
Polymers29,0541
Non-polymers1603
Water2,126118
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-4 kcal/mol
Surface area15350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.520, 104.520, 104.520
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-517-

HOH

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Components

#1: Protein Polyhedrin fused with CLN025 / C-polyhedrin


Mass: 29053.986 Da / Num. of mol.: 1 / Fragment: UNP residues 2-71, UNP residues 77-248
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bombyx mori cypovirus 1, (gene. exp.) synthetic construct (others)
Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P11041
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.65 Å3/Da / Density % sol: 25.25 %
Crystal growTemperature: 293 K / Method: in cell / Details: in cell crystallization

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 5, 2019
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 19331 / % possible obs: 100 % / Redundancy: 211.2 % / CC1/2: 0.98 / Net I/σ(I): 5.84
Reflection shellResolution: 1.75→1.76 Å / Num. unique obs: 489 / CC1/2: 0.319

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PHENIX1.19.2-4158refinement
XSCALEdata scaling
MOLREPphasing
Coot0.8.9.2 ELmodel building
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OH6

2oh6


Resolution: 1.75→42.707 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.922 / SU B: 2.799 / SU ML: 0.085 / Cross valid method: FREE R-VALUE / ESU R: 0.157 / ESU R Free: 0.134
RfactorNum. reflection% reflection
Rfree0.2091 1923 9.948 %
Rwork0.173 17408 -
all0.176 --
obs-19331 99.99 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 9.137 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.75→42.707 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2046 0 12 118 2176
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132111
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171802
X-RAY DIFFRACTIONr_angle_refined_deg1.5441.6472864
X-RAY DIFFRACTIONr_angle_other_deg1.3721.5714185
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2595251
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.17422.423130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.99115325
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4851513
X-RAY DIFFRACTIONr_chiral_restr0.0750.2256
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022430
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02481
X-RAY DIFFRACTIONr_nbd_refined0.2030.2315
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1650.21517
X-RAY DIFFRACTIONr_nbtor_refined0.1690.2995
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0710.2853
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0950.271
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1980.231
X-RAY DIFFRACTIONr_nbd_other0.1960.2136
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1380.232
X-RAY DIFFRACTIONr_mcbond_it0.7730.8991009
X-RAY DIFFRACTIONr_mcbond_other0.7710.8981008
X-RAY DIFFRACTIONr_mcangle_it1.2691.3441259
X-RAY DIFFRACTIONr_mcangle_other1.2691.3451260
X-RAY DIFFRACTIONr_scbond_it1.1371.0481102
X-RAY DIFFRACTIONr_scbond_other1.1371.0481103
X-RAY DIFFRACTIONr_scangle_it1.7971.5231605
X-RAY DIFFRACTIONr_scangle_other1.7961.5231606
X-RAY DIFFRACTIONr_lrange_it2.66910.3482269
X-RAY DIFFRACTIONr_lrange_other2.62410.2942259
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.7960.3841430.4481286X-RAY DIFFRACTION100
1.796-1.8450.3511370.3211260X-RAY DIFFRACTION100
1.845-1.8980.3381320.2451203X-RAY DIFFRACTION100
1.898-1.9570.2111280.1941161X-RAY DIFFRACTION100
1.957-2.0210.1841280.1721137X-RAY DIFFRACTION100
2.021-2.0920.1681230.1531119X-RAY DIFFRACTION100
2.092-2.1710.186950.1481066X-RAY DIFFRACTION100
2.171-2.2590.2021300.1441011X-RAY DIFFRACTION100
2.259-2.360.1841090.15971X-RAY DIFFRACTION100
2.36-2.4750.1881310.143913X-RAY DIFFRACTION100
2.475-2.6080.1691060.141901X-RAY DIFFRACTION100
2.608-2.7660.168760.125864X-RAY DIFFRACTION100
2.766-2.9570.193820.131822X-RAY DIFFRACTION100
2.957-3.1930.18730.133742X-RAY DIFFRACTION100
3.193-3.4980.136720.126703X-RAY DIFFRACTION100
3.498-3.9090.17730.118616X-RAY DIFFRACTION100
3.909-4.5120.165600.124560X-RAY DIFFRACTION100
4.512-5.5210.198550.192476X-RAY DIFFRACTION100
5.521-7.7860.366450.319372X-RAY DIFFRACTION100
7.786-42.7070.742250.563225X-RAY DIFFRACTION99.6016

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