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Yorodumi- PDB-1r8h: Comparison of the structure and DNA binding properties of the E2 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1r8h | ||||||
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Title | Comparison of the structure and DNA binding properties of the E2 proteins from an oncogenic and a non-oncogenic human papillomavirus | ||||||
Components | Regulatory protein E2 | ||||||
Keywords | TRANSCRIPTION / REPLICATION / Anti-parallel beta-barrel / DNA-binding domain | ||||||
Function / homology | Function and homology information viral DNA genome replication / regulation of DNA replication / DNA replication / DNA-binding transcription factor activity / nucleotide binding / DNA-templated transcription / host cell nucleus / DNA binding Similarity search - Function | ||||||
Biological species | Human papillomavirus type 6a | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.9 Å | ||||||
Authors | Dell, G. / Wilkinson, K.W. / Tranter, R. / Parish, J. / Brady, R.L. / Gaston, K. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 Title: Comparison of the structure and DNA-binding properties of the E2 proteins from an oncogenic and a non-oncogenic human papillomavirus. Authors: Dell, G. / Wilkinson, K.W. / Tranter, R. / Parish, J. / Leo Brady, R. / Gaston, K. | ||||||
History |
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Remark 999 | SEQUENCE AUTHORS INFORMED THAT SEQUENCING OF A NUMBER OF RELATED VIRUSES SHOWS THAT THE AMINO ACID ...SEQUENCE AUTHORS INFORMED THAT SEQUENCING OF A NUMBER OF RELATED VIRUSES SHOWS THAT THE AMINO ACID RESIDUE IN THIS POSITION OFTEN DIFFERS BETWEEN ISOLATES DUE TO POLYMORPHISM OF THE GENE. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1r8h.cif.gz | 130.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1r8h.ent.gz | 111.5 KB | Display | PDB format |
PDBx/mmJSON format | 1r8h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r8/1r8h ftp://data.pdbj.org/pub/pdb/validation_reports/r8/1r8h | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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5 |
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6 |
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7 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Beg label comp-ID: SER / End label comp-ID: LEU / Auth seq-ID: 281 - 366 / Label seq-ID: 1 - 87
NCS ensembles :
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-Components
#1: Protein | Mass: 10240.854 Da / Num. of mol.: 6 / Fragment: DNA-binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human papillomavirus type 6a / Genus: Alphapapillomavirus / Species: Human papillomavirus - 6 / Gene: E2 / Plasmid: pKK223-3 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-blue / References: UniProt: Q84294 #2: Chemical | ChemComp-PO4 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.69 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Ammonium sulfate, sodium chloride, sodium hepes, beta-mercaptoethanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 20, 2001 |
Radiation | Monochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. all: 45471 / Num. obs: 42743 / % possible obs: 94 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 1.9→1.97 Å / % possible all: 58.8 |
Reflection | *PLUS Lowest resolution: 20 Å / % possible obs: 93.2 % / Redundancy: 3 % / Rmerge(I) obs: 0.044 |
Reflection shell | *PLUS % possible obs: 58.8 % / Redundancy: 1.4 % / Rmerge(I) obs: 0.221 / Mean I/σ(I) obs: 2.5 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.926 / SU B: 4.009 / SU ML: 0.115 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.192 / ESU R Free: 0.182 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.692 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20 /
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Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.2628 / Rfactor Rwork: 0.2031 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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