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Yorodumi- PDB-1rqy: 9-amino-[N-(2-dimethylamino)proply]-acridine-4-carboxamide bound ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rqy | ||||||||||||||||||
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Title | 9-amino-[N-(2-dimethylamino)proply]-acridine-4-carboxamide bound to d(CGTACG)2 | ||||||||||||||||||
Components | 5'-D(CP*Keywords | DNA / B-DNA / cytosine exchange / quadruplex / acridine / unusual intercalation | Function / homology | Chem-7AD / : / DNA | Function and homology information Method | X-RAY DIFFRACTION / refinement / Resolution: 1.55 Å | Authors | Adams, A. / Guss, J.M. / Denny, W.A. / Wakelin, L.P. | Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2004 | Title: Structure of 9-amino-[N-(2-dimethylamino)propyl]acridine-4-carboxamide bound to d(CGTACG)(2): a comparison of structures of d(CGTACG)(2) complexed with intercalatorsin the presence of cobalt. Authors: Adams, A. / Guss, J.M. / Denny, W.A. / Wakelin, L.P. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rqy.cif.gz | 20.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rqy.ent.gz | 11.9 KB | Display | PDB format |
PDBx/mmJSON format | 1rqy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1rqy_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 1rqy_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 1rqy_validation.xml.gz | 3.9 KB | Display | |
Data in CIF | 1rqy_validation.cif.gz | 4.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rq/1rqy ftp://data.pdbj.org/pub/pdb/validation_reports/rq/1rqy | HTTPS FTP |
-Related structure data
Related structure data | 1fn1S 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 on special symmetry positions |
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-Components
#1: DNA chain | Mass: 1809.217 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Chemical | #3: Chemical | #4: Chemical | #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 Å3/Da / Density % sol: 37.91 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: sodium cacodylate, magnesium acetate, cobalt chloride, spermine, MPD, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 285K | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: AREA DETECTOR / Date: Mar 18, 1998 / Details: focusing mirror optics |
Radiation | Monochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→40 Å / Num. all: 4786 / Num. obs: 4786 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.8 % / Biso Wilson estimate: 20.6 Å2 / Rsym value: 0.077 / Net I/σ(I): 12 |
Reflection shell | Resolution: 1.55→1.61 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 3.8 / Num. unique all: 383 / Rsym value: 0.26 / % possible all: 81.7 |
-Processing
Software |
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Refinement | Method to determine structure: refinement Starting model: PDB entry 1FN1 Resolution: 1.55→40 Å / Num. parameters: 1235 / Num. restraintsaints: 2833 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56
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Refine analyze | Num. disordered residues: 3 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 269.25 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.6 Å /
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