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- PDB-5exy: Crystal structure of in cellulo recombinant CPV1 Polyhedra -

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Basic information

Entry
Database: PDB / ID: 5exy
TitleCrystal structure of in cellulo recombinant CPV1 Polyhedra
ComponentsPolyhedrin
KeywordsVIRAL PROTEIN / in vivo crystal / in cellulo data collection
Function / homologyCypovirus polyhedrin, Cypovirus 1 type / Cypovirus polyhedrin protein / viral occlusion body / host cell cytoplasm / ADENOSINE-5'-TRIPHOSPHATE / CYTIDINE-5'-TRIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Polyhedrin
Function and homology information
Biological speciesBombyx mori cytoplasmic polyhedrosis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 Å
AuthorsBoudes, M. / Garriga, D. / Coulibaly, F.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2016
Title: A pipeline for structure determination of in vivo-grown crystals using in cellulo diffraction.
Authors: Boudes, M. / Garriga, D. / Fryga, A. / Caradoc-Davies, T. / Coulibaly, F.
History
DepositionNov 24, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _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 / _struct_ref_seq_dif.details

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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)30,0098
Polymers28,3871
Non-polymers1,6227
Water3,657203
1
A: Polyhedrin
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)360,11096
Polymers340,64812
Non-polymers19,46384
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 area78150 Å2
ΔGint-609 kcal/mol
Surface area128210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.180, 103.180, 103.180
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-595-

HOH

21A-603-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Polyhedrin / / C-polyhedrin


Mass: 28387.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bombyx mori cytoplasmic polyhedrosis virus
Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P11041

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Non-polymers , 6 types, 210 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE / Cytidine triphosphate


Mass: 483.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O14P3
#6: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O

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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: 1.61 Å3/Da / Density % sol: 23.71 %
Crystal growTemperature: 300 K / Method: in cell
Details: in vivo crystallization in the cytoplasm of the cell

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Data collection

DiffractionMean temperature: 100 K
Ambient temp details: In cellulo data collection. X-ray beam collimated to 10x10 microns.
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 6, 2014
RadiationMonochromator: Double crystal (Si111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→30 Å / Num. obs: 26475 / % possible obs: 99.6 % / Redundancy: 5.9 % / Biso Wilson estimate: 8.12 Å2 / Rmerge(I) obs: 0.249 / Rpim(I) all: 0.111 / Rrim(I) all: 0.257 / Χ2: 1.04 / Net I/av σ(I): 7.632 / Net I/σ(I): 4.3 / Num. measured all: 155448
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allΧ2% possible allRrim(I) all
1.55-1.614.80.93726010.5190.4660.95999.4
1.61-1.675.50.87626090.6070.4050.95899.80.969
1.67-1.755.70.70226660.7330.3160.97799.80.774
1.75-1.846.10.54926070.8370.2390.96799.50.601
1.84-1.956.10.39226290.9070.170.99899.70.429
1.95-2.16.10.28226550.9520.1221.05699.90.308
2.1-2.326.10.22526510.9660.0981.10199.80.246
2.32-2.656.20.20526430.970.0891.1431000.224
2.65-3.346.10.1626700.9790.0691.15199.40.175
3.34-3060.09627440.990.0421.049990.105

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
Coot0.8.1model building
PDB_EXTRACT3.15data extraction
BUSTER2.10.1refinement
BUSTER2.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2OH5

2oh5


Resolution: 1.55→24.32 Å / Cor.coef. Fo:Fc: 0.9671 / Cor.coef. Fo:Fc free: 0.9501 / SU R Cruickshank DPI: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.074 / SU Rfree Blow DPI: 0.076 / SU Rfree Cruickshank DPI: 0.076
RfactorNum. reflection% reflectionSelection details
Rfree0.1669 2750 10.39 %RANDOM
Rwork0.1283 ---
obs0.1321 26475 99.4 %-
Displacement parametersBiso max: 97.99 Å2 / Biso mean: 8.16 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.129 Å
Refinement stepCycle: final / Resolution: 1.55→24.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2009 0 132 203 2344
Biso mean--17.7 15.98 -
Num. residues----248
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d905SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes61HARMONIC2
X-RAY DIFFRACTIONt_gen_planes677HARMONIC5
X-RAY DIFFRACTIONt_it4120HARMONIC20
X-RAY DIFFRACTIONt_nbd4SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion264SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5137SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4120HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg7359HARMONIC21.08
X-RAY DIFFRACTIONt_omega_torsion4.85
X-RAY DIFFRACTIONt_other_torsion15.05
LS refinement shellResolution: 1.55→1.61 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2261 315 10.85 %
Rwork0.1812 2588 -
all0.1861 2903 -
obs--99.4 %

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