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Yorodumi- PDB-1a2e: CRYSTAL STRUCTURE OF A DOUBLE-STRANDED DNA DECAMER CONTAINING A C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1a2e | ||||||
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Title | CRYSTAL STRUCTURE OF A DOUBLE-STRANDED DNA DECAMER CONTAINING A CISPLATIN INTERSTRAND CROSS-LINK ADDUCT | ||||||
Components |
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Keywords | DNA / ANTITUMOR DRUG / CIS-DDP / INTERSTRAND CROSS-LINK | ||||||
Function / homology | Cisplatin / DNA Function and homology information | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.63 Å | ||||||
Authors | Coste, F. / Zelwer, C. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 1999 Title: Crystal structure of a double-stranded DNA containing a cisplatin interstrand cross-link at 1.63 A resolution: hydration at the platinated site. Authors: Coste, F. / Malinge, J.M. / Serre, L. / Shepard, W. / Roth, M. / Leng, M. / Zelwer, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a2e.cif.gz | 23.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a2e.ent.gz | 14.7 KB | Display | PDB format |
PDBx/mmJSON format | 1a2e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a2/1a2e ftp://data.pdbj.org/pub/pdb/validation_reports/a2/1a2e | HTTPS FTP |
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-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: 2931.917 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: PT(CPT) CROSSLINKS N7(G5) AND N7(G15) |
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#2: DNA chain | Mass: 3159.079 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: PT(CPT) CROSSLINKS N7(G5) AND N7(G15) |
#3: Chemical | ChemComp-CPT / |
#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: 2.34 Å3/Da / Density % sol: 56 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.2 / Details: pH 6.20 | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 56 % | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 6 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: LURE / Beamline: DW21B / Wavelength: 1.0711 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1997 / Details: MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0711 Å / Relative weight: 1 |
Reflection | Resolution: 1.63→46.13 Å / Num. obs: 7353 / % possible obs: 93.1 % / Observed criterion σ(I): 4 / Redundancy: 3.5 % / Rmerge(I) obs: 0.037 / Rsym value: 0.037 / Net I/σ(I): 6 |
Reflection shell | Resolution: 1.63→1.72 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.063 / Mean I/σ(I) obs: 12 / Rsym value: 0.049 / % possible all: 91 |
Reflection | *PLUS Num. obs: 7333 / % possible obs: 97 % / Num. measured all: 60517 |
Reflection shell | *PLUS Redundancy: 3.1 % / Mean I/σ(I) obs: 11.1 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.63→20 Å / Num. parameters: 2176 / Num. restraintsaints: 2201 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: NUCLSQ
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-223 | |||||||||||||||||||||||||||||||||
Refine analyze | Occupancy sum hydrogen: 479.67 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.63→20 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-96 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.203 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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