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- PDB-6y5z: Structure of apo Human Polyomavirus 12 VP1 -

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Basic information

Entry
Database: PDB / ID: 6y5z
TitleStructure of apo Human Polyomavirus 12 VP1
ComponentsCapsid protein VP1
KeywordsVIRAL PROTEIN / Major Capsid Protein / Polyomavirus
Function / homologyCapsid protein VP1,Polyomavirus / Polyomavirus capsid protein VP1 superfamily / Polyomavirus coat protein / Double-stranded DNA virus, group I, capsid / T=7 icosahedral viral capsid / host cell nucleus / virion attachment to host cell / structural molecule activity / Capsid protein VP1
Function and homology information
Biological speciesHuman polyomavirus 12
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.549 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
DepositionFeb 26, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
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: Capsid protein VP1
BBB: Capsid protein VP1
CCC: Capsid protein VP1
DDD: Capsid protein VP1
EEE: Capsid protein VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,83319
Polymers153,5435
Non-polymers1,28914
Water27,7251539
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26190 Å2
ΔGint-159 kcal/mol
Surface area45570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.223, 136.416, 85.379
Angle α, β, γ (deg.)90.000, 109.565, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Capsid protein VP1


Mass: 30708.664 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human polyomavirus 12 / Gene: VP1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: M4T5D3
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1539 / 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: 2.28 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: Tacsimate, PEG 3350

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.07 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Apr 30, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 1.549→44.05 Å / Num. obs: 181696 / % possible obs: 95.31 % / Redundancy: 3.8 % / Biso Wilson estimate: 16.35 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.056 / Net I/σ(I): 16.44
Reflection shellResolution: 1.549→1.64 Å / Mean I/σ(I) obs: 2.89 / Num. unique obs: 28058 / CC1/2: 0.855 / Rrim(I) all: 0.456

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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: 1.549→44.047 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.966 / WRfactor Rfree: 0.163 / WRfactor Rwork: 0.138 / SU B: 1.309 / SU ML: 0.046 / Average fsc free: 0.9501 / Average fsc work: 0.9559 / Cross valid method: FREE R-VALUE / ESU R: 0.069 / ESU R Free: 0.07
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1692 3634 2 %
Rwork0.1427 178061 -
all0.143 --
obs-181695 95.103 %
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: 17.014 Å2
Baniso -1Baniso -2Baniso -3
1--0.174 Å20 Å20.067 Å2
2---0.199 Å20 Å2
3---0.259 Å2
Refinement stepCycle: LAST / Resolution: 1.549→44.047 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10154 0 84 1539 11777
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01310664
X-RAY DIFFRACTIONr_bond_other_d0.0020.0179676
X-RAY DIFFRACTIONr_angle_refined_deg1.5481.65414577
X-RAY DIFFRACTIONr_angle_other_deg1.4211.56722489
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.82651380
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.2422.465499
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.29151667
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2381558
X-RAY DIFFRACTIONr_chiral_restr0.0750.21425
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211950
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022160
X-RAY DIFFRACTIONr_nbd_refined0.2050.21746
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1850.29553
X-RAY DIFFRACTIONr_nbtor_refined0.1650.25137
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.24703
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.21111
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3580.213
X-RAY DIFFRACTIONr_nbd_other0.1270.282
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1570.244
X-RAY DIFFRACTIONr_mcbond_it1.2091.6455363
X-RAY DIFFRACTIONr_mcbond_other1.2031.6445362
X-RAY DIFFRACTIONr_mcangle_it1.8692.4586701
X-RAY DIFFRACTIONr_mcangle_other1.8692.4586702
X-RAY DIFFRACTIONr_scbond_it1.7591.815301
X-RAY DIFFRACTIONr_scbond_other1.7591.8115302
X-RAY DIFFRACTIONr_scangle_it2.6542.6467843
X-RAY DIFFRACTIONr_scangle_other2.6532.6467844
X-RAY DIFFRACTIONr_lrange_it4.49420.9911925
X-RAY DIFFRACTIONr_lrange_other4.49420.98911925
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
1.549-1.5890.2252490.219122360.219140870.9060.988.62780.193
1.589-1.6320.2162550.193124620.193137050.9240.92392.79090.167
1.632-1.680.2322500.182122730.183133890.9150.93193.5320.154
1.68-1.7310.22450.178120000.178129640.9370.9494.45390.149
1.731-1.7880.1922390.159117070.16125860.9420.95394.9150.132
1.788-1.8510.1952320.151113680.152122000.9410.95795.0820.126
1.851-1.920.1832250.145110030.146117380.9560.96295.65510.123
1.92-1.9990.172150.14105580.141112420.9630.96695.82810.121
1.999-2.0870.1712090.138102230.139108760.9630.9795.91760.123
2.087-2.1890.1731990.13697610.136103880.9630.9795.87990.121
2.189-2.3070.1541900.12693150.12798230.9690.97496.76270.114
2.307-2.4460.1571800.1388100.1393460.9670.97396.19090.12
2.446-2.6150.1531700.13483560.13487720.9670.97297.19560.127
2.615-2.8230.1581590.13277930.13281940.9690.97497.04660.128
2.823-3.0920.1561460.13571500.13675310.9660.97396.87960.137
3.092-3.4540.171320.13364710.13468120.9670.97596.93190.141
3.454-3.9850.1631170.13657180.13660280.9650.97496.79830.15
3.985-4.870.129980.11948200.1251140.9820.98296.16740.141
4.87-6.8460.173790.15738460.15739820.9710.97698.56860.181
6.846-44.0470.195450.18121910.18122660.9610.96198.67610.214

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