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Yorodumi- PDB-1k2l: STRUCTURAL CHARACTERIZATION OF BISINTERCALATION IN HIGHER-ORDER D... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1k2l | ||||||||||||||||||
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Title | STRUCTURAL CHARACTERIZATION OF BISINTERCALATION IN HIGHER-ORDER DNA AT A JUNCTION-LIKE QUADRUPLEX | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA / DNA Strand Exchange / quadruplex / bisintercalation | Function / homology | Chem-BDC / : / DNA | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | Authors | Teixeira, S.C.M. / Thorpe, J.H. / Todd, A.K. / Powell, H.R. / Adams, A. / Wakelin, L.P.G. / Denny, W.A. / Cardin, C.J. | Citation | Journal: J.MOL.BIOL. / Year: 2002 | Title: Structural Characterisation of Bisintercalation in Higher-order DNA at a Junction-like Quadruplex Authors: Teixeira, S.C.M. / Thorpe, J.H. / Todd, A.K. / Powell, H.R. / Adams, A. / Wakelin, L.P.G. / Denny, W.A. / Cardin, C.J. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1k2l.cif.gz | 19.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k2l.ent.gz | 10.3 KB | Display | PDB format |
PDBx/mmJSON format | 1k2l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k2/1k2l ftp://data.pdbj.org/pub/pdb/validation_reports/k2/1k2l | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
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-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: 1809.217 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Chemical | #3: Chemical | ChemComp-BDC / | #4: 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: 2.28 Å3/Da / Density % sol: 41.47 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Sodium cacodylate buffer, magnesium acetate, cobalt chloride, spermine, MPD, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 285.0K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 285 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.979 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 15, 1996 |
Radiation | Monochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.28→13.5 Å / Num. all: 2063 / Num. obs: 2063 / % possible obs: 88.06 % / Observed criterion σ(F): 2 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.071 / Net I/σ(I): 11.57 |
Reflection shell | Resolution: 2.28→2.36 Å / % possible all: 93.8 |
Reflection | *PLUS Highest resolution: 2.35 Å / Rmerge(I) obs: 0.074 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→9 Å / Num. parameters: 848 / Num. restraintsaints: 1140 / Cross valid method: FREE R / σ(F): 4 / Stereochemistry target values: ENGH AND HUBER
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Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 264 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.48 Å /
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 9 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.3094 / Rfactor Rwork: 0.2385 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: s_angle_d |