+Open data
-Basic information
Entry | Database: PDB / ID: 306d | ||||||||||||||||||
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Title | SIDE-BY-SIDE BINDING OF DISTAMYCIN MOLECULES TO D(ICITACIC) | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / B-DNA / DOUBLE HELIX / COMPLEXED WITH DRUG / DOUBLE DRUG IN THE MINOR GROOVE | Function / homology | DISTAMYCIN A / DNA | Function and homology information Method | X-RAY DIFFRACTION / DIRECT REFINEMENT / Resolution: 1.6 Å | Authors | Chen, X. / Ramakrishnan, B. / Sundaralingam, M. | Citation | Journal: J.Mol.Biol. / Year: 1997 Title: Crystal structures of the side-by-side binding of distamycin to AT-containing DNA octamers d(ICITACIC) and d(ICATATIC). Authors: Chen, X. / Ramakrishnan, B. / Sundaralingam, M. #1: Journal: Nat.Struct.Biol. / Year: 1994 Title: Binding of two Distamycin A Molecules in the Minor Groove of an Alternating B-DNA Authors: Chen, X. / Ramakrishnan, B. / Rao, S.T. / Sundaralingam, M. #2: Journal: Nat.Struct.Biol. / Year: 1995 Title: Crystal Structures of B-Form DNA-RNA Chimers Complexed with Distamycin Authors: Chen, X. / Ramakrishnan, B. / Sundaralingam, M. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 306d.cif.gz | 16.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb306d.ent.gz | 9.8 KB | Display | PDB format |
PDBx/mmJSON format | 306d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 306d_validation.pdf.gz | 398.2 KB | Display | wwPDB validaton report |
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Full document | 306d_full_validation.pdf.gz | 400.1 KB | Display | |
Data in XML | 306d_validation.xml.gz | 1.7 KB | Display | |
Data in CIF | 306d_validation.cif.gz | 2.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/06/306d ftp://data.pdbj.org/pub/pdb/validation_reports/06/306d | HTTPS FTP |
-Related 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: 2382.563 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: Chemical | ChemComp-DMY / |
#3: Chemical | ChemComp-MG / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.17 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION, HANGING DROP / Temp details: ROOM TEMPERATURE | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS pH: 7 | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU |
Detector | Type: SIEMENS-NICOLET / Detector: AREA DETECTOR / Date: Feb 18, 1994 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.5→5.1 Å / Num. all: 20233 / Num. obs: 3778 / % possible obs: 92 % / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rsym value: 0.048 |
Reflection | *PLUS % possible obs: 92 % / Rmerge(I) obs: 0.048 |
-Processing
Software |
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Refinement | Method to determine structure: DIRECT REFINEMENT Starting model: GDHB25 Resolution: 1.6→5.1 Å / σ(F): 2
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Displacement parameters | Biso mean: 16.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine Biso |
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Refinement step | Cycle: LAST / Resolution: 1.6→5.1 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.6 Å / Lowest resolution: 5.1 Å / σ(F): 2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 16.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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