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- PDB-5a9a: Crystal structure of Simulium ubiquitum CPV20 polyhedra -

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Basic information

Entry
Database: PDB / ID: 5a9a
TitleCrystal structure of Simulium ubiquitum CPV20 polyhedra
ComponentsPOLYHEDRIN
KeywordsVIRAL PROTEIN / INSECT VIRUS OCCLUSION BODY / MICROCRYSTAL
Function / homologyCypovirus polyhedrin / Cypovirus polyhedrin / URIDINE 5'-TRIPHOSPHATE / Polyhedrin
Function and homology information
Biological speciesSIMULIUM UBIQUITUM CYPOVIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.822 Å
AuthorsJi, X. / Axford, D. / Owen, R. / Evans, G. / Ginn, H.M. / Sutton, G. / Stuart, D.I.
CitationJournal: J.Struct.Biol. / Year: 2015
Title: Polyhedra Structures and the Evolution of the Insect Viruses.
Authors: Ji, X. / Axford, D. / Owen, R. / Evans, G. / Ginn, H.M. / Sutton, G. / Stuart, D.I.
History
DepositionJul 17, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Database references
Revision 1.2Oct 23, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: pdbx_database_status / struct_conn / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3May 1, 2024Group: 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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)28,6802
Polymers28,1961
Non-polymers4841
Water2,900161
1
A: POLYHEDRIN
hetero molecules

A: POLYHEDRIN
hetero molecules

A: POLYHEDRIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,0406
Polymers84,5873
Non-polymers1,4523
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation5_555z,x,y1
Buried area11110 Å2
ΔGint-38.5 kcal/mol
Surface area34340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.360, 103.360, 103.360
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


Mass: 28195.736 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SIMULIUM UBIQUITUM CYPOVIRUS / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q0MX25
#2: Chemical ChemComp-UTP / URIDINE 5'-TRIPHOSPHATE


Mass: 484.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15N2O15P3 / Comment: UTP*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 51

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Sample preparation

CrystalDensity Matthews: 1.6 Å3/Da / Density % sol: 24.6 % / Description: NONE
Crystal growpH: 7.5 / Details: pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.979
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.82→51.7 Å / Num. obs: 16582 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 10 % / Biso Wilson estimate: 11.7 Å2 / Rmerge(I) obs: 0.34 / Net I/σ(I): 5.4
Reflection shellResolution: 1.82→1.87 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 1.1 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MODELS OF POLYHEDRA STRUCTURE OF CPV5, CPV4, CPV1, CPV14, CPV15 AND CPV19

Resolution: 1.822→42.197 Å / SU ML: 0.45 / σ(F): 1.34 / Phase error: 17.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1899 837 5.1 %
Rwork0.1566 --
obs0.1583 16568 99.88 %
Solvent computationShrinkage radii: 0.89 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.791 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 22 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.822→42.197 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1979 0 29 161 2169
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032057
X-RAY DIFFRACTIONf_angle_d0.8272788
X-RAY DIFFRACTIONf_dihedral_angle_d14.329771
X-RAY DIFFRACTIONf_chiral_restr0.052280
X-RAY DIFFRACTIONf_plane_restr0.004373
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.822-1.93620.32411320.26052594X-RAY DIFFRACTION100
1.9362-2.08570.23011570.19782579X-RAY DIFFRACTION100
2.0857-2.29560.21021410.16782599X-RAY DIFFRACTION100
2.2956-2.62770.18491350.14812614X-RAY DIFFRACTION100
2.6277-3.31040.17951410.13362624X-RAY DIFFRACTION100
3.3104-42.20780.15481310.14052721X-RAY DIFFRACTION100

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