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- PDB-5gql: Crystal structure of Wild Type Cypovirus Polyhedra -

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Basic information

Entry
Database: PDB / ID: 5gql
TitleCrystal structure of Wild Type Cypovirus Polyhedra
ComponentsPolyhedrin
KeywordsVIRAL PROTEIN / In vivo protein crystal / Polyhedra
Function / homologyCypovirus polyhedrin, Cypovirus 1 type / Cypovirus polyhedrin protein / viral occlusion body / host cell cytoplasm / ADENOSINE-5'-TRIPHOSPHATE / CYTIDINE-5'-TRIPHOSPHATE / Polyhedrin
Function and homology information
Biological speciesBombyx mori cypovirus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsAbe, S. / Tabe, H. / Ijiri, H. / Yamashita, K. / Hirata, K. / Mori, H. / Ueno, T.
CitationJournal: ACS Nano / Year: 2017
Title: Crystal Engineering of Self-Assembled Porous Protein Materials in Living Cells
Authors: Abe, S. / Tabe, H. / Ijiri, H. / Yamashita, K. / Hirata, K. / Atsumi, K. / Shimoi, T. / Akai, M. / Mori, H. / Kitagawa, S. / Ueno, T.
History
DepositionAug 7, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2017Group: Database references
Revision 1.2Feb 26, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)29,5247
Polymers28,3871
Non-polymers1,1366
Water2,378132
1
A: Polyhedrin
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)354,28584
Polymers340,64812
Non-polymers13,63872
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_566z,-x+1,-y+11
crystal symmetry operation7_665-z+1,-x+1,y1
crystal symmetry operation8_656-z+1,x,-y+11
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_656-y+1,z,-x+11
crystal symmetry operation11_566y,-z+1,-x+11
crystal symmetry operation12_665-y+1,-z+1,x1
Buried area64950 Å2
ΔGint-332 kcal/mol
Surface area124790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.328, 103.328, 103.328
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-529-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Polyhedrin / C-polyhedrin / Cypovirus polyhedrin protein


Mass: 28387.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bombyx mori cypovirus 1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P11041

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Non-polymers , 6 types, 138 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE


Mass: 483.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O14P3
#5: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.62 Å3/Da / Density % sol: 24.04 %
Crystal growTemperature: 300 K / Method: in cell / Details: in vivo crystallization

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 0.6888 Å
DetectorType: RAYONIX MX325HE / Detector: CCD / Date: Jul 19, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6888 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. obs: 17724 / % possible obs: 100 % / Redundancy: 4.7 % / Net I/σ(I): 7.8
Reflection shellResolution: 1.78→1.81 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OH6

2oh6


Resolution: 1.78→32.68 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.927 / SU B: 3.071 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.158 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20118 898 5.1 %RANDOM
Rwork0.16365 ---
obs0.16558 16710 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 6.934 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.78→32.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2009 0 67 132 2208
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192145
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6041.9612914
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5165250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.62623.75116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.95115327
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.3871514
X-RAY DIFFRACTIONr_chiral_restr0.1070.2293
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211678
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.3790.521993
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.6540.7771240
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.9280.7791149
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined2.7665.3273275
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.782→1.828 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 65 -
Rwork0.226 1193 -
obs--98.98 %

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