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- PDB-5exz: Crystal structure of purified recombinant CPV1 Polyhedra -

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Basic information

Entry
Database: PDB / ID: 5exz
TitleCrystal structure of purified recombinant CPV1 Polyhedra
ComponentsPolyhedrin
KeywordsVIRAL PROTEIN / in vivo crystal / polyhedrin
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 cypovirus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 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
Revision 1.2Oct 9, 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)30,0098
Polymers28,3871
Non-polymers1,6227
Water3,117173
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 area78730 Å2
ΔGint-612 kcal/mol
Surface area128260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.170, 103.170, 103.170
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-571-

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 cypovirus 1 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P11041

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Non-polymers , 6 types, 180 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.: 3 / Source method: obtained synthetically / Formula: Mg
#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-CTP / CYTIDINE-5'-TRIPHOSPHATE


Mass: 483.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O14P3
#6: 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
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 1.61 Å3/Da / Density % sol: 23.69 %
Crystal growTemperature: 300 K / Method: in cell
Details: The crystals used to determine this structure were directly purified from cells, in vivo crystallization in the cytoplasm of the cell

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: beam collimated to 10 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: 1.9→30 Å / Num. obs: 13734 / % possible obs: 94.5 % / Redundancy: 3.3 % / Biso Wilson estimate: 5.01 Å2 / Rmerge(I) obs: 0.268 / Rpim(I) all: 0.165 / Rrim(I) all: 0.322 / Χ2: 1.031 / Net I/av σ(I): 4.81 / Net I/σ(I): 4.5 / Num. measured all: 42463
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible allRmerge(I) obs
1.9-1.973.41.912500.7090.3480.6881.04993.4
2.02-2.13.412510.7580.2910.5751.00194.60.49
2.1-2.23.312890.7930.260.5071.04795.20.432
2.2-2.313.312580.8120.2310.4520.9695.60.385
2.31-2.463.312870.840.2180.42195.90.356
2.46-2.653.212820.8720.1950.3761.00196.10.318
2.65-2.913.312860.9080.1570.3081.0495.80.263
2.91-3.333.412700.9440.1260.2461.21893.50.208
3.33-4.23.312580.9680.0840.1640.99492.90.139
4.2-303.413080.9820.0630.1250.99692.20.107

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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
BUSTER2.10.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OH5

2oh5


Resolution: 1.9→27.57 Å / Cor.coef. Fo:Fc: 0.9423 / Cor.coef. Fo:Fc free: 0.8957 / SU R Cruickshank DPI: 0.198 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.216 / SU Rfree Blow DPI: 0.162 / SU Rfree Cruickshank DPI: 0.16
RfactorNum. reflection% reflectionSelection details
Rfree0.2036 1380 10.05 %RANDOM
Rwork0.1465 ---
obs0.152 13732 94.41 %-
Displacement parametersBiso max: 63.05 Å2 / Biso mean: 7.6 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: 0.17 Å
Refinement stepCycle: final / Resolution: 1.9→27.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2003 0 96 173 2272
Biso mean--14.67 11.96 -
Num. residues----248
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d955SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes60HARMONIC2
X-RAY DIFFRACTIONt_gen_planes307HARMONIC5
X-RAY DIFFRACTIONt_it2157HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion262SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies1HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2778SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2157HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2950HARMONIC21.04
X-RAY DIFFRACTIONt_omega_torsion4.06
X-RAY DIFFRACTIONt_other_torsion2.81
LS refinement shellResolution: 1.9→2.05 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2394 297 10.79 %
Rwork0.1744 2456 -
all0.1811 2753 -
obs--94.41 %

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