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- PDB-2ayb: Crystal structure of HPV6a E2 DNA Binding Domain bound to a 16 ba... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2ayb | ||||||
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Title | Crystal structure of HPV6a E2 DNA Binding Domain bound to a 16 base pair DNA target | ||||||
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![]() | TRANSCRIPTION/DNA / ![]() ![]() ![]() | ||||||
Function / homology | ![]() viral DNA genome replication / ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Hooley, E. / Brady, R.L. / Gaston, K. | ||||||
![]() | ![]() Title: The recognition of local DNA conformation by the human papillomavirus type 6 E2 protein. Authors: Hooley, E. / Fairweather, V. / Clarke, A.R. / Gaston, K. / Brady, R.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 69.1 KB | Display | ![]() |
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PDB format | ![]() | 48.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2ayeC ![]() 2aygC ![]() 1jj4S ![]() 1r8hS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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: HIS / End label comp-ID: HIS / Refine code: 1 / Auth seq-ID: 283 - 364 / Label seq-ID: 3 - 85
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Details | The biological assembly is a protein dimer bound to double stranded DNA |
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Components
#1: DNA chain | Mass: 4898.191 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Protein | Mass: 10240.854 Da / Num. of mol.: 2 / Fragment: C Terminal Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #3: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 53 % | ||||||||||||||||||||
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: tri-Sodium citrate dihydrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: BRUKER SMART 6000 / Detector: CCD / Date: May 20, 2005 / Details: mirrors |
Radiation | Monochromator: Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 3.2→65.23 Å / Num. all: 5168 / Num. obs: 4928 / % possible obs: 99.37 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 22.5 % / Rmerge(I) obs: 0.138 / Net I/σ(I): 19.8 |
Reflection shell | Resolution: 3.2→3.28 Å / Redundancy: 22.5 % / Rmerge(I) obs: 0.387 / Mean I/σ(I) obs: 5.2 / Num. unique all: 362 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: Protein of PDB entry 1R8H DNA of PDB entry 1JJ4 Resolution: 3.2→65.23 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.843 / SU B: 33.517 / SU ML: 0.402 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.632 / 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: 41.3 Å2
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Refinement step | Cycle: LAST / Resolution: 3.2→65.23 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: 693 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 3.204→3.287 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth seq-ID: 281 - 366 / Label seq-ID: 1 - 87
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