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- PDB-3s7x: Unassembled Washington University Polyomavirus VP1 Pentamer R198K... -

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Basic information

Entry
Database: PDB / ID: 3s7x
TitleUnassembled Washington University Polyomavirus VP1 Pentamer R198K Mutant
ComponentsMajor capsid protein VP1
KeywordsVIRAL PROTEIN / jelly-roll fold / antiparallel beta sandwich / major capsid protein
Function / homology
Function and homology information


T=7 icosahedral viral capsid / endocytosis involved in viral entry into host cell / virion attachment to host cell / host cell nucleus / structural molecule activity
Similarity search - Function
Capsid protein VP1,Polyomavirus / Polyomavirus Vp1; Chain A / Capsid protein VP1,Polyomavirus / Polyomavirus capsid protein VP1 superfamily / Polyomavirus coat protein / Double-stranded DNA virus, group I, capsid / Sandwich / Mainly Beta
Similarity search - Domain/homology
Major capsid protein VP1
Similarity search - Component
Biological speciesWU Polyomavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsNeu, U. / Wang, J. / Stehle, T.
CitationJournal: J.Virol. / Year: 2011
Title: Structures of the major capsid proteins of the human KI and WU polyomaviruses.
Authors: Neu, U. / Wang, J. / Macejak, D. / Garcea, R.L. / Stehle, T.
History
DepositionMay 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Major capsid protein VP1
B: Major capsid protein VP1
C: Major capsid protein VP1
D: Major capsid protein VP1
E: Major capsid protein VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,86720
Polymers145,1145
Non-polymers75315
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20980 Å2
ΔGint-165 kcal/mol
Surface area48810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.200, 166.200, 127.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
12A
22B
32C
42D
52E

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1113A31 - 63
2113B31 - 63
3113C31 - 63
4113D31 - 63
5113E31 - 63
1213A67 - 104
2213B67 - 104
3213C67 - 104
4213D67 - 104
5213E67 - 104
1313A117 - 138
2313B117 - 138
3313C117 - 138
4313D117 - 138
5313E117 - 138
1413A140 - 182
2413B140 - 182
3413C140 - 182
4413D140 - 182
5413E140 - 182
1513A185 - 294
2513B185 - 294
3513C185 - 294
4513D185 - 294
5513E185 - 294
1126A1
2126B1
3126C1
4126D1
5126E1

NCS ensembles :
ID
1
2

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Components

#1: Protein
Major capsid protein VP1 / Major structural protein VP1


Mass: 29022.891 Da / Num. of mol.: 5 / Fragment: UNP residues 34-296 / Mutation: R198K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) WU Polyomavirus / Gene: VP1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A5HBD5
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
Has protein modificationY
Sequence detailsTHE R198K MUTATION WAS INTRODUCED INTO THE WILD-TYPE PROTEIN TO REMOVE A NON-CANONICAL THROMBIN ...THE R198K MUTATION WAS INTRODUCED INTO THE WILD-TYPE PROTEIN TO REMOVE A NON-CANONICAL THROMBIN CLEAVAGE SITE TO OBTAIN A HOMOGENEOUS SAMPLE FOR CRYSTALLIZATION

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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: 3.04 Å3/Da / Density % sol: 59.48 %
Crystal growTemperature: 282 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M trisodium citrate, 0.1 M HEPES pH 7.5, 20 % (v/v) isopropanol, VAPOR DIFFUSION, SITTING DROP, temperature 282K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 15, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.9→40 Å / Num. all: 40144 / Num. obs: 39647 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.096 / Net I/σ(I): 11.1
Reflection shellResolution: 2.9→2.98 Å / Rmerge(I) obs: 0.578 / Mean I/σ(I) obs: 1.8 / % possible all: 99.4

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→43.36 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.906 / SU B: 17.497 / SU ML: 0.315 / Cross valid method: THROUGHOUT / ESU R Free: 0.394 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25296 3038 7.6 %RANDOM
Rwork0.234 ---
obs0.23545 36689 98.73 %-
all-39647 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.169 Å2
Baniso -1Baniso -2Baniso -3
1-1.68 Å20 Å20 Å2
2--1.68 Å20 Å2
3----3.36 Å2
Refinement stepCycle: LAST / Resolution: 2.9→43.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9935 0 40 0 9975
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02210209
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1971.96913942
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.42751291
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.88323.918416
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.367151556
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9321560
X-RAY DIFFRACTIONr_chiral_restr0.0820.21593
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0227794
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_it1.63726488
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.008410535
X-RAY DIFFRACTIONr_scbond_it1.89623719
X-RAY DIFFRACTIONr_scangle_it3.35443407
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A960tight positional0.020.05
2B960tight positional0.020.05
3C960tight positional0.020.05
4D960tight positional0.020.05
5E960tight positional0.020.05
1A885loose positional0.025
2B885loose positional0.025
3C885loose positional0.025
4D885loose positional0.025
5E885loose positional0.025
1A960tight thermal0.040.5
2B960tight thermal0.040.5
3C960tight thermal0.040.5
4D960tight thermal0.040.5
5E960tight thermal0.040.5
1A885loose thermal0.0310
2B885loose thermal0.0310
3C885loose thermal0.0310
4D885loose thermal0.0310
5E885loose thermal0.0310
LS refinement shellResolution: 2.897→2.972 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 215 -
Rwork0.37 2649 -
obs--98.35 %

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