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Yorodumi- PDB-144d: MINOR GROOVE BINDING OF SN6999 TO AN ALKYLATED DNA: MOLECULAR STR... -
+Open data
-Basic information
Entry | Database: PDB / ID: 144d | ||||||||||||||||||
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Title | MINOR GROOVE BINDING OF SN6999 TO AN ALKYLATED DNA: MOLECULAR STRUCTURE OF D(CGC[E6G]AATTCGCG)-SN6999 COMPLEX | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / B-DNA / DOUBLE HELIX / COMPLEXED WITH DRUG / MODIFIED | Function / homology | Chem-SN6 / DNA / DNA (> 10) | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 2.25 Å | Authors | Gao, Y.-G. / Sriram, M. / Denny, W.A. / Wang, A.H.-J. | Citation | Journal: Biochemistry / Year: 1993 | Title: Minor groove binding of SN6999 to an alkylated DNA: molecular structure of d(CGC[e6G]AATTCGCG)-SN6999 complex. Authors: Gao, Y.G. / Sriram, M. / Denny, W.A. / Wang, A.H. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 144d.cif.gz | 27.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb144d.ent.gz | 16.7 KB | Display | PDB format |
PDBx/mmJSON format | 144d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 144d_validation.pdf.gz | 404.1 KB | Display | wwPDB validaton report |
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Full document | 144d_full_validation.pdf.gz | 426.7 KB | Display | |
Data in XML | 144d_validation.xml.gz | 6.1 KB | Display | |
Data in CIF | 144d_validation.cif.gz | 7.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/44/144d ftp://data.pdbj.org/pub/pdb/validation_reports/44/144d | 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: 3691.445 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Chemical | ChemComp-SN6 / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.25 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION / 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 | Ambient temp details: ROOM TEMPERATURE |
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Diffraction source | Source: ROTATING ANODE |
Detector | Type: RIGAKU AFC-5R / Detector: DIFFRACTOMETER |
Radiation | Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Highest resolution: 2.25 Å / Num. obs: 1618 / Observed criterion σ(F): 2 |
Reflection | *PLUS Highest resolution: 2.25 Å / % possible obs: 50 % / Observed criterion σ(F): 2 |
-Processing
Software | Name: NUCLSQ / Classification: refinement | ||||||||||||
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Refinement | Resolution: 2.25→10 Å / σ(F): 2 /
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Refine Biso |
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Refinement step | Cycle: LAST / Resolution: 2.25→10 Å
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Refinement | *PLUS Highest resolution: 2.25 Å / Lowest resolution: 10 Å / σ(F): 2 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS | ||||||||||||
Refine LS restraints | *PLUS Type: n_bond_d / Dev ideal: 0.019 |