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- PDB-6y9i: Structure of apo Chimpanzee Polyomavirus VP1 -

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Basic information

Entry
Database: PDB / ID: 6y9i
TitleStructure of apo Chimpanzee Polyomavirus VP1
ComponentsMajor Capsid Protein VP1
KeywordsVIRAL PROTEIN / Major Capsid Protein / Polyomavirus
Biological speciesChimpanzee polyomavirus Bob
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsStroh, L.J. / Rustmeier, N.H. / Stehle, T.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)FOR2327 Germany
CitationJournal: Mbio / Year: 2020
Title: Structural Basis and Evolution of Glycan Receptor Specificities within the Polyomavirus Family.
Authors: Stroh, L.J. / Rustmeier, N.H. / Blaum, B.S. / Botsch, J. / Rossler, P. / Wedekink, F. / Lipkin, W.I. / Mishra, N. / Stehle, T.
History
DepositionMar 9, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2020Group: Database references / Derived calculations / Category: citation / pdbx_struct_conn_angle / struct_conn
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_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_label_seq_id
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Major Capsid Protein VP1
BBB: Major Capsid Protein VP1
CCC: Major Capsid Protein VP1
DDD: Major Capsid Protein VP1
EEE: Major Capsid Protein VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,00915
Polymers159,7665
Non-polymers24310
Water17,060947
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22480 Å2
ΔGint-231 kcal/mol
Surface area49310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.410, 82.190, 82.660
Angle α, β, γ (deg.)68.614, 77.361, 77.488
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Major Capsid Protein VP1


Mass: 31953.271 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chimpanzee polyomavirus Bob / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 947 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.42 Å3/Da / Density % sol: 49.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Sodium acetate trihydrate, PEG 3,350, 1,5-Diaminopentane dihydrochloride

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00003 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Apr 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.9→46.46 Å / Num. obs: 117709 / % possible obs: 99.4 % / Redundancy: 6.95 % / Biso Wilson estimate: 32.2 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.15 / Net I/σ(I): 9.83
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 1.61 / Num. unique obs: 8633 / CC1/2: 0.57 / Rrim(I) all: 0.135 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FMG

4fmg


Resolution: 1.9→46.456 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.946 / WRfactor Rfree: 0.202 / WRfactor Rwork: 0.16 / SU B: 4.034 / SU ML: 0.113 / Average fsc free: 0.8978 / Average fsc work: 0.9133 / Cross valid method: FREE R-VALUE / ESU R: 0.139 / ESU R Free: 0.133
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2134 5886 5 %
Rwork0.1706 111823 -
all0.173 --
obs-117709 99.592 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 28.057 Å2
Baniso -1Baniso -2Baniso -3
1--0.216 Å2-0.601 Å20.382 Å2
2--0.19 Å2-0.499 Å2
3----0.353 Å2
Refinement stepCycle: LAST / Resolution: 1.9→46.456 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10524 0 10 947 11481
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01310856
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179964
X-RAY DIFFRACTIONr_angle_refined_deg1.571.64514777
X-RAY DIFFRACTIONr_angle_other_deg1.3141.5723138
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.62751412
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.31922.701485
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14151730
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.551556
X-RAY DIFFRACTIONr_chiral_restr0.0720.21436
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212277
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022127
X-RAY DIFFRACTIONr_nbd_refined0.1920.21918
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1860.29686
X-RAY DIFFRACTIONr_nbtor_refined0.1620.25082
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.24992
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2781
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0490.26
X-RAY DIFFRACTIONr_metal_ion_refined0.0240.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2540.219
X-RAY DIFFRACTIONr_nbd_other0.2540.268
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.220.28
X-RAY DIFFRACTIONr_mcbond_it2.2782.8955651
X-RAY DIFFRACTIONr_mcbond_other2.2742.8945650
X-RAY DIFFRACTIONr_mcangle_it3.2834.3217062
X-RAY DIFFRACTIONr_mcangle_other3.2834.3227063
X-RAY DIFFRACTIONr_scbond_it2.8733.0915205
X-RAY DIFFRACTIONr_scbond_other2.8733.0915206
X-RAY DIFFRACTIONr_scangle_it4.2144.5427715
X-RAY DIFFRACTIONr_scangle_other4.2144.5427715
X-RAY DIFFRACTIONr_lrange_it5.79234.53111737
X-RAY DIFFRACTIONr_lrange_other5.73434.23711588
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.9-1.9490.34310.27481830.27687080.7650.78898.92050.256
1.949-2.0030.2884250.23780870.23985760.8270.85999.25370.216
2.003-2.060.2634110.22977930.23182560.8610.86499.37020.203
2.06-2.1240.2724000.20776090.2180530.8670.89399.45360.18
2.124-2.1930.2473860.19873380.277610.8910.90799.52330.172
2.193-2.270.2443770.18871500.19175530.8980.91199.65580.161
2.27-2.3560.2223640.17469200.17773070.910.92899.68520.147
2.356-2.4510.2293470.17266010.17569640.9110.92999.77020.146
2.451-2.560.2333360.18563770.18767220.9010.9299.86610.158
2.56-2.6850.2493180.17760510.1863860.9020.92999.73380.152
2.685-2.8290.2213060.15358100.15661180.9370.95199.96730.135
2.829-30.2062880.16154770.16457750.9410.94999.82680.144
3-3.2070.2062720.15451600.15754430.9420.95499.79790.143
3.207-3.4620.1792510.15147770.15350320.9560.96299.92050.146
3.462-3.790.1882320.15144070.15346450.950.9699.87080.152
3.79-4.2340.1682120.13940170.14142400.9620.96799.74060.145
4.234-4.8830.171840.12935020.13137160.9640.97199.19270.139
4.883-5.9630.1961550.16629450.16831100.9520.95499.67850.18
5.963-8.3650.2121220.18223110.18424390.9430.95299.7540.198
8.365-46.4560.213690.19413080.19513800.9440.94799.78260.22

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