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- PDB-4ots: Crystal Structure of isolated Operophtera brumata CPV18 -

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Basic information

Entry
Database: PDB / ID: 4ots
TitleCrystal Structure of isolated Operophtera brumata CPV18
ComponentsPolyhedrin
KeywordsVIRAL PROTEIN / microcrystals / polyhedra / occlusion body
Function / homologyCypovirus polyhedrin, Cypovirus 1 type / Cypovirus polyhedrin protein / ATP binding / metal ion binding / ADENOSINE-5'-TRIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Polyhedrin
Function and homology information
Biological speciesOperophtera brumata cypovirus 18
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.704 Å
AuthorsStuart, D.I. / Sutton, G.C. / Axford, D. / Ji, X.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: In cellulo structure determination of a novel cypovirus polyhedrin.
Authors: Axford, D. / Ji, X. / Stuart, D.I. / Sutton, G.
History
DepositionFeb 14, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)29,3915
Polymers28,3011
Non-polymers1,0904
Water4,342241
1
A: Polyhedrin
hetero molecules

A: Polyhedrin
hetero molecules

A: Polyhedrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,17415
Polymers84,9043
Non-polymers3,27012
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation12_555-y,-z,x1
Buried area13470 Å2
ΔGint-104 kcal/mol
Surface area34790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.794, 102.794, 102.794
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-597-

HOH

21A-623-

HOH

31A-638-

HOH

41A-640-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Polyhedrin


Mass: 28301.373 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Operophtera brumata cypovirus 18 / Plasmid: pOPIN / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: Q30C70

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Non-polymers , 5 types, 245 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#4: 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
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 20

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Sample preparation

CrystalDensity Matthews: 1.6 Å3/Da / Density % sol: 23.08 %
Crystal growTemperature: 301 K / pH: 7.5
Details: Crystals formed naturally within the cytoplasm and were purified from cells, pH 7.5, temperature 301K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 28, 2011 / Details: mirrors
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.7→72.686 Å / Num. all: 19343 / Num. obs: 19343 / % possible obs: 97.2 % / Observed criterion σ(F): 1.34 / Observed criterion σ(I): 1.34
Reflection shellHighest resolution: 1.7 Å

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Processing

Software
NameVersionClassification
GDAdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
FastDPdata reduction
Blenddata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.704→27.473 Å / SU ML: 0.12 / σ(F): 1.34 / Phase error: 11.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1315 992 5.13 %RANDOM
Rwork0.1002 ---
obs0.1018 19327 97.13 %-
all-19327 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.704→27.473 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2001 0 65 241 2307
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062124
X-RAY DIFFRACTIONf_angle_d1.1692901
X-RAY DIFFRACTIONf_dihedral_angle_d17.923778
X-RAY DIFFRACTIONf_chiral_restr0.045291
X-RAY DIFFRACTIONf_plane_restr0.006372
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.704-1.79410.1896980.15632224X-RAY DIFFRACTION82
1.7941-1.90650.20011460.13132608X-RAY DIFFRACTION99
1.9065-2.05360.14451440.10652689X-RAY DIFFRACTION100
2.0536-2.26020.14541590.08992645X-RAY DIFFRACTION100
2.2602-2.58710.10291470.08892687X-RAY DIFFRACTION100
2.5871-3.25860.11531550.08662698X-RAY DIFFRACTION100
3.2586-27.47640.10661430.09062784X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -20.9564 Å / Origin y: 8.6787 Å / Origin z: -34.0137 Å
111213212223313233
T0.004 Å20.0022 Å2-0.0001 Å2-0.0075 Å2-0.0021 Å2--0.0096 Å2
L0.0028 °2-0.0004 °20.0002 °2-0.0062 °2-0.0023 °2--0.0008 °2
S0.0009 Å °0.0039 Å °-0.0025 Å °0.0004 Å °0.0007 Å °0.0015 Å °0.0015 Å °-0 Å °0.0017 Å °
Refinement TLS groupSelection details: all

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