+Open data
-Basic information
Entry | Database: PDB / ID: 423d | ||||||||||||||||||
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Title | 5'-D(*AP*CP*CP*GP*AP*CP*GP*TP*CP*GP*GP*T)-3' | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / DOUBLE HELIX | Function / homology | DNA / DNA (> 10) | Function and homology information Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | Authors | Rozenberg, H. / Rabinovich, D. / Frolow, F. / Hegde, R.S. / Shakked, Z. | Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1998 | Title: Structural code for DNA recognition revealed in crystal structures of papillomavirus E2-DNA targets. Authors: Rozenberg, H. / Rabinovich, D. / Frolow, F. / Hegde, R.S. / Shakked, Z. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 423d.cif.gz | 29.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb423d.ent.gz | 19 KB | Display | PDB format |
PDBx/mmJSON format | 423d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/23/423d ftp://data.pdbj.org/pub/pdb/validation_reports/23/423d | HTTPS FTP |
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-Related 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: DNA chain | Mass: 3663.392 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Chemical | ChemComp-MG / #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: 2.228 Å3/Da / Density % sol: 46.7 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7 Details: pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 19 ℃ / Method: vapor diffusion, hanging drop / Details: used to seeding | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-C |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jan 3, 1997 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER, GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.6→23.6 Å / Num. all: 8888 / Num. obs: 8888 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 50.8 |
Reflection shell | Resolution: 1.6→1.62 Å / Redundancy: 1.95 % / Rmerge(I) obs: 0.235 / Mean I/σ(I) obs: 4.9 / % possible all: 95 |
Reflection | *PLUS Observed criterion σ(F): 2 / Num. measured all: 68426 |
Reflection shell | *PLUS % possible obs: 95 % / Num. unique obs: 8888 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: IDEAL B-DNA Resolution: 1.6→23.6 Å / Num. parameters: 2703 / Num. restraintsaints: 11946 / σ(F): 0 / σ(I): 0
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Solvent computation | Solvent model: MOEWS & KRETSINGER: J.MOL.BIOL. 91, 201-228 (1973) | |||||||||||||||||||||||||||||||||
Refine analyze | Occupancy sum non hydrogen: 644.67 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→23.6 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 2 / Rfactor obs: 0.174 / Lowest resolution: 23.6 Å / % reflection Rfree: 5.7 % | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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