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- PDB-1ilc: DNA Bending by an Adenine-Thymine Tract and Its Role in Gene Regu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ilc | ||||||||||||||||||
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Title | DNA Bending by an Adenine-Thymine Tract and Its Role in Gene Regulation. | ||||||||||||||||||
![]() | 5'-D(*![]() DNA / B-DNA DOUBLE HELIX / DODECAMER DUPLEX / HPV E2 DNA TARGET | Function / homology | DNA / DNA (> 10) | ![]() Method | ![]() ![]() ![]() Hizver, J. / Rozenberg, H. / Frolow, F. / Rabinovich, D. / Shakked, Z. | ![]() ![]() Title: DNA bending by an adenine--thymine tract and its role in gene regulation. Authors: Hizver, J. / Rozenberg, H. / Frolow, F. / Rabinovich, D. / Shakked, Z. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 49.1 KB | Display | ![]() |
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PDB format | ![]() | 34.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 382.8 KB | Display | ![]() |
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Full document | ![]() | 385.4 KB | Display | |
Data in XML | ![]() | 5.9 KB | Display | |
Data in CIF | ![]() | 7.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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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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Components
#1: DNA chain | Mass: 3662.404 Da / Num. of mol.: 6 / Source method: obtained synthetically / Details: Human papillomavirus E2 DNA target #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 57 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7 Details: MPD, magnesium chloride, spermine.4HCl, Na cacodylate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 292.0K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 19 ℃ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Nov 10, 1997 / Details: Yale-type mirrors |
Radiation | Monochromator: Ni filter + Yale-type mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→19 Å / Num. all: 9810 / Num. obs: 9810 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 25.8 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.654 / Mean I/σ(I) obs: 2 / Num. unique all: 491 / Rsym value: 0.654 / % possible all: 95 |
Reflection | *PLUS Num. measured all: 36389 / Rmerge(I) obs: 0.051 |
Reflection shell | *PLUS Highest resolution: 2.2 Å / % possible obs: 95 % / Rmerge(I) obs: 0.564 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: Fiber model of B-DNA Resolution: 2.2→19 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Parkinson et al. Details: REFINEMENT STARTED WITH X-PLOR 3.1 USING B-DNA FIBER MODEL ALL DATA INCLUDED. REFINEMENT CONTINUED IN SHELXL-97 WITH THE OPTION HOPE FOR ANISOTROPIC SCALING TO CORRECT SIGNIFICANT ANISOTROPY ...Details: REFINEMENT STARTED WITH X-PLOR 3.1 USING B-DNA FIBER MODEL ALL DATA INCLUDED. REFINEMENT CONTINUED IN SHELXL-97 WITH THE OPTION HOPE FOR ANISOTROPIC SCALING TO CORRECT SIGNIFICANT ANISOTROPY IN THE DATA. THE CORRECTED OBSERVED STRUCTURE FACTORS WITH F<0 WERE EXCLUDED FROM REFINEMENT. REFINEMENT FURTHER CONTINUED WITH X-PLOR 3.1.
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Displacement parameters | Biso mean: 30.1 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→19 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.3 Å /
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Xplor file | Serial no: 1 / Param file: PARAM_NDBX.DNA / Topol file: TOP_NDBX.DNA | |||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 8474 / % reflection Rfree: 5 % / Rfactor obs: 0.224 / Rfactor Rfree: 0.292 / Rfactor Rwork: 0.224 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.37 / Rfactor Rwork: 0.33 / Rfactor obs: 0.33 |