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Yorodumi- PDB-482d: RELEASE OF THE CYANO MOIETY IN THE CRYSTAL STRUCTURE OF N-CYANOME... -
+Open data
-Basic information
Entry | Database: PDB / ID: 482d | ||||||||||||||||||
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Title | RELEASE OF THE CYANO MOIETY IN THE CRYSTAL STRUCTURE OF N-CYANOMETHYL-N-(2-METHOXYETHYL)-DAUNOMYCIN COMPLEXED WITH D(CGATCG) | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA / RIGHT HANDED DNA / DOUBLE HELIX / COMPLEXED WITH DRUG / DEOXYRIBONUCLEIC ACID | Function / homology | N-HYDROXYMETHYL-N-(2-METHOXYETHYL)-DAUNOMYCIN / DNA | Function and homology information Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.54 Å | Authors | Saminadin, P. / Dautant, A. / Mondon, M. / Langlois D'Estaintot, B. / Courseille, C. / Precigoux, G. | Citation | Journal: Eur.J.Biochem. / Year: 2000 Title: Release of the cyano moiety in the crystal structure of N-cyanomethyl-N-(2-methoxyethyl)-daunomycin complexed with d(CGATCG). Authors: Saminadin, P. / Dautant, A. / Mondon, M. / Langlois D'estaintot, B. / Courseille, C. / Precigoux, G. #1: Journal: Eur.J.Biochem. / Year: 1998 Title: Degradation of the Morpholino Ring in the Crystal Structure of Cyanomorpholinodoxorubicin Authors: Ettorre, A. / Cirilli, M. / Ughetto, G. #2: Journal: Biochemistry / Year: 1990 Title: Structural Comparison of Anticancer Drug-DNA Complexes. Adriamycin and Daunomycin Authors: Frederick, C.A. / Williams, L.D. / Ughetto, G. / Van Der Marel, G.A. / Van Boom, J.H. / Rich, A. / Wang, A.H.-J. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 482d.cif.gz | 15 KB | Display | PDBx/mmCIF format |
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PDB format | pdb482d.ent.gz | 8.4 KB | Display | PDB format |
PDBx/mmJSON format | 482d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 482d_validation.pdf.gz | 721.8 KB | Display | wwPDB validaton report |
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Full document | 482d_full_validation.pdf.gz | 723.3 KB | Display | |
Data in XML | 482d_validation.xml.gz | 3.3 KB | Display | |
Data in CIF | 482d_validation.cif.gz | 3.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/82/482d ftp://data.pdbj.org/pub/pdb/validation_reports/82/482d | 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: 1809.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: COMPLEXED WITH (2-METHOXYETHYL)-DAUNOMYCIN |
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#2: Chemical | ChemComp-DM9 / |
#3: Water | ChemComp-HOH / |
Nonpolymer details | N-CYANOMETHYL-N-(2-METHOXYETHYL)-DAUNOMYCIN WAS USED IN CRYSTALLIZATION SET-UP. DEGRADATION OF THIS ...N-CYANOMETHY |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 44.5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: CRYSTALS WERE OBTAINED FROM A SOLUTION THAT CONTAINED MPD, LICL, MGCL2, SODIUM CACODYLATE, COBALT HEXAMINE, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 6.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 1999 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.54→12.6 Å / Num. obs: 3327 / % possible obs: 95.5 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 15.3 Å2 / Rmerge(I) obs: 0.046 / Rsym value: 0.046 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 1.54→1.57 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.158 / Mean I/σ(I) obs: 3.9 / Rsym value: 0.158 / % possible all: 92.3 |
Reflection shell | *PLUS % possible obs: 92.3 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: SEE REMARK 1 REFERENCE 2 Resolution: 1.54→12.6 Å / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 19.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.54→12.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.54→1.58 Å / Total num. of bins used: 15
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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