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- PDB-7xhr: Crystal structure of Wild Type Cypovirus Polyhedra produced by ce... -

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Basic information

Entry
Database: PDB / ID: 7xhr
TitleCrystal structure of Wild Type Cypovirus Polyhedra produced by cell-free protein synthesis
ComponentsPolyhedrin
KeywordsVIRAL PROTEIN / cell-free crystallization / in cell crystal
Function / homologyCypovirus polyhedrin, Cypovirus 1 type / Cypovirus polyhedrin protein / viral occlusion body / host cell cytoplasm / ACETYL GROUP / Polyhedrin
Function and homology information
Biological speciesBombyx mori cypovirus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.801 Å
AuthorsAbe, S. / Tanaka, J. / Kojima, M. / Hirata, K. / Yamashita, K. / Ueno, T.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP18H05421 Japan
Japan Society for the Promotion of Science (JSPS)JP19H02830 Japan
Japan Science and TechnologyJPMJTR20U1 Japan
CitationJournal: Sci Rep / Year: 2022
Title: Cell-free protein crystallization for nanocrystal structure determination.
Authors: Abe, S. / Tanaka, J. / Kojima, M. / Kanamaru, S. / Hirata, K. / Yamashita, K. / Kobayashi, A. / Ueno, T.
History
DepositionApr 10, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 1, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4413
Polymers28,3611
Non-polymers802
Water2,504139
1
A: Polyhedrin
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)341,28936
Polymers340,33512
Non-polymers95424
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 area55730 Å2
ΔGint-282 kcal/mol
Surface area127950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.610, 103.610, 103.610
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-536-

HOH

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Components

#1: Protein Polyhedrin / C-polyhedrin


Mass: 28361.277 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bombyx mori cypovirus 1 / Production host: Triticum aestivum (bread wheat) / References: UniProt: P11041
#2: Chemical ChemComp-ACE / ACETYL GROUP


Mass: 44.053 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 24.73 %
Crystal growTemperature: 293 K / Method: small tubes / Details: cell-free crystallization

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 17297 / % possible obs: 100 % / Redundancy: 399 % / CC1/2: 0.9899 / Net I/σ(I): 5.5
Reflection shellResolution: 1.8→1.81 Å / Mean I/σ(I) obs: 1.53 / Num. unique obs: 414 / CC1/2: 0.5326
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PHENIX1.18.2refinement
CrystFELdata scaling
Cootmodel building
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5gqm

5gqm


Resolution: 1.801→42.299 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.227 / SU ML: 0.094 / Cross valid method: FREE R-VALUE / ESU R: 0.155 / ESU R Free: 0.128
RfactorNum. reflection% reflection
Rfree0.184 1742 10.071 %
Rwork0.1495 15555 -
all0.153 --
obs-17297 99.988 %
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: 15.194 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.801→42.299 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2006 0 4 139 2149
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132066
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171768
X-RAY DIFFRACTIONr_angle_refined_deg1.531.6422804
X-RAY DIFFRACTIONr_angle_other_deg1.3981.5724108
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3665248
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.34222.269130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.35915326
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5031514
X-RAY DIFFRACTIONr_chiral_restr0.0770.2250
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022389
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02473
X-RAY DIFFRACTIONr_nbd_refined0.1950.2361
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1720.21609
X-RAY DIFFRACTIONr_nbtor_refined0.1720.2996
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.2903
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.2102
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2190.249
X-RAY DIFFRACTIONr_nbd_other0.20.2183
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1260.230
X-RAY DIFFRACTIONr_mcbond_it0.9631.515991
X-RAY DIFFRACTIONr_mcbond_other0.9611.514990
X-RAY DIFFRACTIONr_mcangle_it1.3892.2671237
X-RAY DIFFRACTIONr_mcangle_other1.3892.2681238
X-RAY DIFFRACTIONr_scbond_it1.6331.7151074
X-RAY DIFFRACTIONr_scbond_other1.6351.7141071
X-RAY DIFFRACTIONr_scangle_it2.5112.4961566
X-RAY DIFFRACTIONr_scangle_other2.5112.4961565
X-RAY DIFFRACTIONr_lrange_it3.38917.6632316
X-RAY DIFFRACTIONr_lrange_other3.31817.5742299
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc workWRfactor Rwork
1.801-1.8480.2871300.29211580.29112880.8320.8320.282
1.848-1.8980.3121230.24710860.25312090.8740.8760.229
1.898-1.9530.2751190.22610880.2312070.8750.8940.203
1.953-2.0130.2631160.19210340.19911500.8880.9180.167
2.013-2.0790.1711150.16610140.16611290.9440.9390.144
2.079-2.1520.2081130.169880.16511010.9390.9460.136
2.152-2.2330.1831050.1539560.15610610.9460.9520.132
2.233-2.3240.1871000.1379110.14210110.9550.9630.119
2.324-2.4270.161000.1298870.1339870.9650.9690.112
2.427-2.5450.19900.1368170.1419070.9570.9650.119
2.545-2.6820.21940.138180.1389120.9440.9650.113
2.682-2.8440.164840.1297500.1338340.9630.9710.114
2.844-3.0390.163810.1267190.138000.9640.9750.113
3.039-3.2810.154770.1276720.1297490.9710.9760.113
3.281-3.5920.134660.1196250.1216910.9810.9820.111
3.592-4.0120.154600.1095530.1136130.9740.9830.106
4.012-4.6260.134580.1245090.1255670.9810.9840.126
4.626-5.6490.153480.1474280.1474760.9780.9820.151
5.649-7.9190.208390.1763330.1793720.9660.970.172
7.919-42.2990.203240.1952090.1962330.9620.9680.2

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