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- PDB-5axv: Crystal Structure of Cypovirus Polyhedra R13K Mutant -

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Basic information

Entry
Database: PDB / ID: 5axv
TitleCrystal Structure of Cypovirus Polyhedra R13K Mutant
ComponentsPolyhedrin
KeywordsSTRUCTURAL PROTEIN / INTRACELLULAR CRYSTAL / NUCLEOTIDE BINDING
Function / homologyCypovirus polyhedrin, Cypovirus 1 type / Cypovirus polyhedrin protein / viral occlusion body / host cell cytoplasm / CYTIDINE-5'-TRIPHOSPHATE / Polyhedrin
Function and homology information
Biological speciesBombyx mori cypovirus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsAbe, S. / Ijiri, H. / Negishi, H. / Yamanaka, H. / Sasaki, K. / Hirata, K. / Mori, H. / Ueno, T.
CitationJournal: Adv. Mater. Weinheim / Year: 2015
Title: Design of Enzyme-Encapsulated Protein Containers by In Vivo Crystal Engineering
Authors: Abe, S. / Ijiri, H. / Negishi, H. / Yamanaka, H. / Sasaki, K. / Hirata, K. / Mori, H. / Ueno, T.
History
DepositionAug 1, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 11, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 1.2Feb 26, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)29,0646
Polymers28,3591
Non-polymers7055
Water2,198122
1
A: Polyhedrin
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)348,76972
Polymers340,31212
Non-polymers8,45860
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 area70010 Å2
ΔGint-259 kcal/mol
Surface area126820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.381, 103.381, 103.381
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein Polyhedrin / C-polyhedrin


Mass: 28359.301 Da / Num. of mol.: 1 / Mutation: R13K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bombyx mori cypovirus 1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P11041
#2: Chemical ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE


Mass: 483.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O14P3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 1.62 Å3/Da / Density % sol: 24.23 %
Crystal growTemperature: 300 K / Method: in cell / pH: 7
Details: IN VIVO CRYSTALLIZATION IN THE CYTOPLASM OF THE CELL, PH 7.0, TEMPERATURE 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 2, 2011
RadiationMonochromator: LIQUID NITROGEN COOLED DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.04→40 Å / Num. obs: 11308 / % possible obs: 93.3 % / Redundancy: 2.8 % / Biso Wilson estimate: 8.1 Å2 / Rsym value: 0.179 / Net I/σ(I): 6.15
Reflection shellResolution: 2.04→2.08 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 2.2 / Rsym value: 0.48 / % possible all: 97.3

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Processing

Software
NameVersionClassification
HKL-2000data scaling
MOLREPphasing
REFMAC5.6.0117refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OH6

2oh6


Resolution: 2.04→36.55 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.91 / SU B: 4.295 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.322 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.206 535 4.7 %RANDOM
Rwork0.149 ---
obs0.152 10749 95.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 7.57 Å2
Refinement stepCycle: LAST / Resolution: 2.04→36.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2007 0 42 122 2171
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.022099
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6531.9442847
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7395246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.44724.035114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.7615326
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4831513
X-RAY DIFFRACTIONr_chiral_restr0.1110.2286
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211650
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
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: 2.04→2.1 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.23 43 -
Rwork0.168 755 -
obs--98.28 %

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