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Yorodumi- PDB-2r5i: Pentamer Structure of Major Capsid Protein L1 of Human Papilloma ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2r5i | ||||||
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Title | Pentamer Structure of Major Capsid Protein L1 of Human Papilloma Virus type 18 | ||||||
Components | L1 protein | ||||||
Keywords | VIRAL PROTEIN / HPV18 / pentamer / type specific epitope / capsid / Capsid protein / Virion | ||||||
Function / homology | Function and homology information T=7 icosahedral viral capsid / endocytosis involved in viral entry into host cell / membrane => GO:0016020 / host cell nucleus / virion attachment to host cell / structural molecule activity Similarity search - Function | ||||||
Biological species | Human papillomavirus type 18 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å | ||||||
Authors | Bishop, B. / Dasgupta, J. / Chen, X.S. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2r5i.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2r5i.ent.gz | 996.1 KB | Display | PDB format |
PDBx/mmJSON format | 2r5i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2r5i_validation.pdf.gz | 622.7 KB | Display | wwPDB validaton report |
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Full document | 2r5i_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 2r5i_validation.xml.gz | 258.9 KB | Display | |
Data in CIF | 2r5i_validation.cif.gz | 336.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r5/2r5i ftp://data.pdbj.org/pub/pdb/validation_reports/r5/2r5i | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 6 / Auth seq-ID: 20 - 475 / Label seq-ID: 1 - 428
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-Components
#1: Protein | Mass: 47591.188 Da / Num. of mol.: 15 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human papillomavirus type 18 / Genus: Alphapapillomavirus / Species: Human papillomavirus - 18 / Gene: L1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q80B70, UniProt: P06794*PLUS |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.79 % |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 |
Detector | Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 3.4→50 Å / Num. obs: 98881 / Redundancy: 3.55 % / Rsym value: 19.6 / Net I/σ(I): 4.4 |
-Processing
Software | Name: REFMAC / Version: 5.2.0019 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.4→40 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.856 / SU B: 30.746 / SU ML: 0.503 / Cross valid method: THROUGHOUT / ESU R Free: 0.657 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.199 Å2
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Refinement step | Cycle: LAST / Resolution: 3.4→40 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3323 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 3.4→3.488 Å / Total num. of bins used: 20
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