+Open data
-Basic information
Entry | Database: PDB / ID: 2dyw | ||||||||||||||||||
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Title | A Backbone binding DNA complex | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA / Platinum / Phosphate Clamp / Anticancer Drug | Function / homology | Chem-A71 / Chem-A72 / DNA / DNA (> 10) | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.13 Å | Authors | Komeda, S. / Moulaei, T. / Woods, K.K. / Chikuma, M. / Farrell, N.P. / Williams, L.D. | Citation | Journal: J.Am.Chem.Soc. / Year: 2006 | Title: A Third Mode of DNA Binding: Phosphate Clamps by a Polynuclear Platinum Complex Authors: Komeda, S. / Moulaei, T. / Woods, K.K. / Chikuma, M. / Farrell, N.P. / Williams, L.D. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dyw.cif.gz | 43.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dyw.ent.gz | 28.7 KB | Display | PDB format |
PDBx/mmJSON format | 2dyw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2dyw_validation.pdf.gz | 457.4 KB | Display | wwPDB validaton report |
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Full document | 2dyw_full_validation.pdf.gz | 483.1 KB | Display | |
Data in XML | 2dyw_validation.xml.gz | 3.9 KB | Display | |
Data in CIF | 2dyw_validation.cif.gz | 5.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dy/2dyw ftp://data.pdbj.org/pub/pdb/validation_reports/dy/2dyw | HTTPS FTP |
-Related structure data
Related structure data | 355dS S: Starting model for refinement |
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Similar structure data |
-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 | #3: Chemical | ChemComp-NA / | #4: Chemical | ChemComp-A72 / | #5: 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: 2.12 Å3/Da / Density % sol: 41.94 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.19mM [d(CGCGAATTCGCG)]2, 0.19mM TriplatinNC, 31mM sodium cacodylate (pH 6.5), 9.6mM magnesium chloride, 6.9% 2-methyl-2,4-pentanediol (MPD), equilibrated against a reservoir of 30% MPD, ...Details: 0.19mM [d(CGCGAATTCGCG)]2, 0.19mM TriplatinNC, 31mM sodium cacodylate (pH 6.5), 9.6mM magnesium chloride, 6.9% 2-methyl-2,4-pentanediol (MPD), equilibrated against a reservoir of 30% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 175 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.05 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 19, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05 Å / Relative weight: 1 |
Reflection | Resolution: 1.07→50 Å / Num. all: 23727 / Num. obs: 21375 / % possible obs: 90.1 % / Observed criterion σ(F): 1 / Redundancy: 12.5 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 355D(NDB entry: bdl084) Resolution: 1.13→5.5 Å / Num. parameters: 5106 / Num. restraintsaints: 5941 Isotropic thermal model: anisotropic: DNA and NO5, isotropic: AH78, AH79 and solvent Cross valid method: FREE R / σ(F): 2 Stereochemistry target values: Gelbin, A., Schneider, B., Clowney, L., Hsieh, S.-H., Olson, W.K., and Berman, H.M. (1996). Geometric parameters in nucleic acids: sugar and phosphate constituents. J. ...Stereochemistry target values: Gelbin, A., Schneider, B., Clowney, L., Hsieh, S.-H., Olson, W.K., and Berman, H.M. (1996). Geometric parameters in nucleic acids: sugar and phosphate constituents. J. Am. Chem. Soc. 118(3), 519-528. Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF)
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Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 647.55 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.13→5.5 Å
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Refine LS restraints |
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LS refinement shell | Highest resolution: 1.13 Å
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