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Yorodumi- PDB-1m6f: Strong Binding in the DNA Minor Groove by an Aromatic Diamidine W... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1m6f | ||||||||||||||||||
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Title | Strong Binding in the DNA Minor Groove by an Aromatic Diamidine With a Shape That Does Not Match the Curvature of the Groove | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / Nucleic acids / minor groove binder / double helix / DNA-drug complex | Function / homology | Chem-CGQ / DNA / DNA (> 10) | Function and homology information Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.78 Å | Authors | Nguyen, B. / Lee, M.P.H. / Hamelberg, D. / Joubert, A. / Bailly, C. / Brun, R. / Neidle, S. / Wilson, W.D. | Citation | Journal: J.Am.Chem.Soc. / Year: 2002 | Title: Strong Binding in the DNA Minor Groove by an Aromatic Diamidine With a Shape That Does Not Match the Curvature of the Groove Authors: Nguyen, B. / Lee, M.P.H. / Hamelberg, D. / Joubert, A. / Bailly, C. / Brun, R. / 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 | 1m6f.cif.gz | 27.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1m6f.ent.gz | 17.4 KB | Display | PDB format |
PDBx/mmJSON format | 1m6f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1m6f_validation.pdf.gz | 739.7 KB | Display | wwPDB validaton report |
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Full document | 1m6f_full_validation.pdf.gz | 722.7 KB | Display | |
Data in XML | 1m6f_validation.xml.gz | 5.2 KB | Display | |
Data in CIF | 1m6f_validation.cif.gz | 6.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m6/1m6f ftp://data.pdbj.org/pub/pdb/validation_reports/m6/1m6f | 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-MG / | #3: Chemical | ChemComp-CGQ / | #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: 2.06 Å3/Da / Density % sol: 40.25 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: MGCL2 2UL OF 75MM, DNA DOUBLE-STRANDED 3UL OF 2MM, MPD 2UL OF 25%, DRUG 2UL OF 4.5MM, SODIUM CACODYLATE 40MM. MPD IN RESERVOIR 700UL OF 50%., pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 104 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 27, 2002 / Details: Yale Focussing Mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→17 Å / Num. obs: 6040 / % possible obs: 92.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 8.8 % / Rmerge(I) obs: 0.047 |
Reflection shell | Resolution: 1.78→1.84 Å / % possible obs: 90.6 % / Rmerge(I) obs: 0.184 / % possible all: 90.6 |
Reflection | *PLUS Num. measured all: 53082 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: DNA PART OF NDB ENTRY GDL009 Resolution: 1.78→10 Å / Cross valid method: THROUGHOUT / σ(F): 4 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.78→10 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 10 Å / Rfactor obs: 0.1988 / Rfactor Rfree: 0.2713 / Rfactor Rwork: 0.2015 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |