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Yorodumi- PDB-1dto: CRYSTAL STRUCTURE OF THE COMPLETE TRANSACTIVATION DOMAIN OF E2 PR... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dto | ||||||
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Title | CRYSTAL STRUCTURE OF THE COMPLETE TRANSACTIVATION DOMAIN OF E2 PROTEIN FROM THE HUMAN PAPILLOMAVIRUS TYPE 16 | ||||||
Components | REGULATORY PROTEIN E2 | ||||||
Keywords | VIRAL PROTEIN / three-helix bundle / beta-sheet | ||||||
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 / SYNCHROTRON / MIR / Resolution: 1.9 Å | ||||||
Authors | Antson, A.A. / Burns, J.E. / Moroz, O.V. / Scott, D.J. / Sanders, C.M. / Bronstein, I.B. / Dodson, G.G. / Wilson, K.S. / Maitland, N. | ||||||
Citation | Journal: Nature / Year: 2000 Title: Structure of the intact transactivation domain of the human papillomavirus E2 protein. Authors: Antson, A.A. / Burns, J.E. / Moroz, O.V. / Scott, D.J. / Sanders, C.M. / Bronstein, I.B. / Dodson, G.G. / Wilson, K.S. / Maitland, N.J. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1998 Title: Expression, Crystallisation and Preliminary X-ray Analysis of the E2 Transactivation Domain from Papillomavirus Type 16 Authors: Burns, J.E. / Moroz, O.V. / Antson, A.A. / Sanders, C.M. / Wilson, K.S. / Maitland, N.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dto.cif.gz | 59.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dto.ent.gz | 42.6 KB | Display | PDB format |
PDBx/mmJSON format | 1dto.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dt/1dto ftp://data.pdbj.org/pub/pdb/validation_reports/dt/1dto | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a dimer constructed from chain A; the symmetry partner is generated by the crystallographic two-fold rotation X-Y,-Y,2/3-Z |
-Components
#1: Protein | Mass: 25698.955 Da / Num. of mol.: 1 / Fragment: TRANSACTIVATION DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human papillomavirus type 16 / Genus: Alphapapillomavirus / Species: Human papillomavirus - 16 / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / 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: 2.4 Å3/Da / Density % sol: 55 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.3 Details: monomethylether PEG 5000, NaCl, isopropanol, triethanolamine,Tris-HCl, DTT, EDTA, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.89 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 15, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.89 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. all: 21751 / Num. obs: 21751 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 30.9 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 25.7 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.339 / Num. unique all: 837 / % possible all: 89.3 |
Reflection | *PLUS |
Reflection shell | *PLUS % possible obs: 89.3 % |
-Processing
Software |
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Refinement | Method to determine structure: MIR Starting model: NONE Resolution: 1.9→30 Å / SU B: 4.1 / SU ML: 0.121 / σ(F): 0 / σ(I): 0 / ESU R: 0.167 / ESU R Free: 0.176 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.9→30 Å
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Refine LS restraints |
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