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Yorodumi- PDB-1eel: STRUCTURE OF A COMPLEX BETWEEN THE DNA SEQUENCE DCGCGAATTCGCG AND... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1eel | ||||||||||||||||||
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Title | STRUCTURE OF A COMPLEX BETWEEN THE DNA SEQUENCE DCGCGAATTCGCG AND BIS[PIPERIDINO-ETHYL]-FURAMIDINE | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA / MINOR GROOVE BINDING LIGAND / B-DNA / BULKY SIDE-CHAINS | Function / homology | Chem-D24 / DNA / DNA (> 10) | Function and homology information Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | Authors | Neidle, S. / Simpson, I.J. | Citation | Journal: J.Mol.Biol. / Year: 2000 | Title: A thermodynamic and structural analysis of DNA minor-groove complex formation. Authors: Mazur, S. / Tanious, F.A. / Ding, D. / Kumar, A. / Boykin, D.W. / Simpson, I.J. / Neidle, S. / Wilson, W.D. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1eel.cif.gz | 25.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1eel.ent.gz | 16 KB | Display | PDB format |
PDBx/mmJSON format | 1eel.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1eel_validation.pdf.gz | 390.9 KB | Display | wwPDB validaton report |
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Full document | 1eel_full_validation.pdf.gz | 393.8 KB | Display | |
Data in XML | 1eel_validation.xml.gz | 2 KB | Display | |
Data in CIF | 1eel_validation.cif.gz | 3.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ee/1eel ftp://data.pdbj.org/pub/pdb/validation_reports/ee/1eel | HTTPS FTP |
-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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-Components
#1: DNA chain | Mass: 3663.392 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Chemical | ChemComp-D24 / | #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: 2.37 Å3/Da / Density % sol: 48.12 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: MPD 3 UL OF 25%, MGCL2 2UL OF 90MM, SPERMINE 1UL OF 10MM, DNA 2UL OF 2MM, LIGAND 2UL OF 3MM, MPD IN RESERVOIR 1ML OF 30%, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 286 K / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Oct 20, 1998 / Details: YALE FOCUSSING MIRRORS |
Radiation | Monochromator: Y / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→12 Å / Num. obs: 3105 / % possible obs: 94.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 6 % / Rmerge(I) obs: 0.033 / Net I/σ(I): 9.6 |
Reflection | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 12 Å / Num. all: 3292 / Num. measured all: 18138 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: DNA PART OF NDB STRUCTURE GDL044 Resolution: 2.4→8 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / Stereochemistry target values: PARKINSON ET AL. / Details: USED SHELX-97 PROCEDURE
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Refinement step | Cycle: LAST / Resolution: 2.4→8 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.4 Å / Rfactor all: 0.184 / Rfactor Rwork: 0.184 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |