[English] 日本語
Yorodumi- PDB-1dl8: CRYSTAL STRUCTURE OF 5-F-9-AMINO-(N-(2-DIMETHYLAMINO)ETHYL)ACRIDI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dl8 | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF 5-F-9-AMINO-(N-(2-DIMETHYLAMINO)ETHYL)ACRIDINE-4-CARBOXAMIDE BOUND TO D(CGTACG)2 | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / INTERCALATION / ACRIDINE | Function / homology | Chem-DA7 / DNA | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 1.55 Å | Authors | Adams, A. / Guss, J.M. / Collyer, C.A. / Denny, W.A. / Wakelin, L.P. | Citation | Journal: Mol.Pharmacol. / Year: 2000 | Title: Acridinecarboxamide topoisomerase poisons: structural and kinetic studies of the DNA complexes of 5-substituted 9-amino-(N-(2-dimethylamino)ethyl)acridine-4-carboxamides. Authors: Adams, A. / Guss, J.M. / Collyer, C.A. / Denny, W.A. / Prakash, A.S. / Wakelin, L.P. History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1dl8.cif.gz | 15.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1dl8.ent.gz | 8.7 KB | Display | PDB format |
PDBx/mmJSON format | 1dl8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dl8_validation.pdf.gz | 967.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1dl8_full_validation.pdf.gz | 974.2 KB | Display | |
Data in XML | 1dl8_validation.xml.gz | 4 KB | Display | |
Data in CIF | 1dl8_validation.cif.gz | 4.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dl/1dl8 ftp://data.pdbj.org/pub/pdb/validation_reports/dl/1dl8 | HTTPS FTP |
-Related structure data
Similar structure data | |
---|---|
Other databases |
|
-Links
-Assembly
Deposited unit |
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
Unit cell |
|
-Components
#1: DNA chain | Mass: 1809.217 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
---|---|---|---|
#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.6 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 6.5 Details: MPD, SODIUM CACODYLATE, SPERMINE, NACL, MGCL2, pH 6.5, VAPOR DIFFUSION, temperature 291K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 / Method: vapor diffusion, sitting drop | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 110 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Mar 20, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→50 Å / Num. all: 3022 / Num. obs: 3006 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.6 % / Biso Wilson estimate: 14.03 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 36.6 |
Reflection shell | Resolution: 1.55→1.61 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.243 / % possible all: 97.3 |
Reflection shell | *PLUS % possible obs: 97.3 % / Mean I/σ(I) obs: 4.3 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Starting model: NDB ID DD0015 Resolution: 1.55→16 Å / Num. parameters: 755 / Num. restraintsaints: 1032 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0
| |||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: MOEWS & KRETSINGER: J.MOL.BIOL. 91(1973) 201-228 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 1 / Occupancy sum non hydrogen: 174.38 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→16 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||
Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 8.3 % / Rfactor Rfree: 0.2615 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|