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- PDB-2r5k: Pentamer Structure of Major Capsid protein L1 of Human Papilloma ... -

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Basic information

Entry
Database: PDB / ID: 2r5k
TitlePentamer Structure of Major Capsid protein L1 of Human Papilloma Virus type 11
ComponentsMajor capsid protein L1
KeywordsVIRAL PROTEIN / HPV11 / Capsid / Pentamer / Type specific epitope / Capsid protein / Late protein / Virion
Function / homology
Function and homology information


T=7 icosahedral viral capsid / endocytosis involved in viral entry into host cell / host cell nucleus / virion attachment to host cell / structural molecule activity
Similarity search - Function
Major capsid L1 (late) superfamily, Papillomavirus / Major capsid L1 (late) protein, Papillomavirus / Major capsid L1 (late) superfamily, Papillomavirus / L1 (late) protein / Polyomavirus Vp1; Chain A / Double-stranded DNA virus, group I, capsid / Sandwich / Mainly Beta
Similarity search - Domain/homology
Major capsid protein L1
Similarity search - Component
Biological speciesHuman papillomavirus type 11
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsBishop, B. / Dasgupta, J. / Chen, X.S.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Crystal structures of four types of human papillomavirus L1 capsid proteins: understanding the specificity of neutralizing monoclonal antibodies.
Authors: Bishop, B. / Dasgupta, J. / Klein, M. / Garcea, R.L. / Christensen, N.D. / Zhao, R. / Chen, X.S.
History
DepositionSep 3, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 2, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Major capsid protein L1
B: Major capsid protein L1
C: Major capsid protein L1
D: Major capsid protein L1
E: Major capsid protein L1


Theoretical massNumber of molelcules
Total (without water)234,7135
Polymers234,7135
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.710, 159.970, 158.440
Angle α, β, γ (deg.)90.00, 101.83, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Major capsid protein L1


Mass: 46942.664 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human papillomavirus type 11 / Genus: Alphapapillomavirus / Species: Human papillomavirus - 6 / Gene: L1 / Production host: Escherichia coli (E. coli) / References: UniProt: P04012

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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: 3.06 Å3/Da / Density % sol: 59.77 %
Crystal growMethod: vapor diffusion / Details: VAPOR DIFFUSION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 45624 / Redundancy: 3.18 % / Rsym value: 19.2 / Net I/σ(I): 5.5

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Processing

SoftwareName: CNS / Version: 1.1 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→48.24 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 230609.54 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.317 7879 9.6 %RANDOM
Rwork0.289 ---
obs0.289 45624 89 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.30466 e/Å3
Displacement parametersBiso mean: 4.1 Å2
Baniso -1Baniso -2Baniso -3
1-1.12 Å20 Å20.03 Å2
2---1.91 Å20 Å2
3---0.79 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.54 Å0.48 Å
Luzzati d res low-5 Å
Luzzati sigma a0.6 Å0.59 Å
Refinement stepCycle: LAST / Resolution: 3.2→48.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16390 0 0 0 16390
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.2→3.4 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.376 1267 9.5 %
Rwork0.357 12001 -
obs--86.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param

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