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Yorodumi- PDB-1by9: CRYSTAL STRUCTURE OF THE E2 DNA-BINDING DOMAIN FROM HUMAN PAPILLO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1by9 | ||||||
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Title | CRYSTAL STRUCTURE OF THE E2 DNA-BINDING DOMAIN FROM HUMAN PAPILLOMAVIRUS TYPE-16: IMPLICATIONS FOR ITS DNA BINDING-SITE SELECTION MECHANISM | ||||||
Components | REGULATORY PROTEIN E2 | ||||||
Keywords | TRANSCRIPTION REGULATION / PAPILLOMAVIRUS / BETA-BARREL | ||||||
Function / homology | Function and homology information host cytoskeleton / 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 16 | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Hegde, R.S. / Androphy, E.J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1998 Title: Crystal structure of the E2 DNA-binding domain from human papillomavirus type 16: implications for its DNA binding-site selection mechanism. Authors: Hegde, R.S. / Androphy, E.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1by9.cif.gz | 26.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1by9.ent.gz | 16.4 KB | Display | PDB format |
PDBx/mmJSON format | 1by9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/by/1by9 ftp://data.pdbj.org/pub/pdb/validation_reports/by/1by9 | HTTPS FTP |
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-Related structure data
Related structure data | 2bopS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 9368.822 Da / Num. of mol.: 1 / Fragment: DNA-BINDING DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human papillomavirus type 16 / Genus: Alphapapillomavirus / Species: Human papillomavirus - 16 / Cell line: BL21 / Gene: E2 / Plasmid: BL21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P03120 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.58 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.2 / Details: pH 6.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Details: MIRRORS |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→99 Å / Num. obs: 4165 / % possible obs: 90.3 % / Observed criterion σ(I): 0 / Redundancy: 8 % / Biso Wilson estimate: 20.4 Å2 / Rsym value: 0.118 |
Reflection | *PLUS % possible obs: 98.8 % / Num. measured all: 32566 / Rmerge(I) obs: 0.118 |
Reflection shell | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 2.28 Å / % possible obs: 99.8 % / Rmerge(I) obs: 0.314 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2BOP Resolution: 2.2→99 Å / Rfactor Rfree error: 0.01 / Data cutoff high rms absF: 454894.2 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / ksol: 0.355 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.4 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.22 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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