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Yorodumi- PDB-1lu5: 2.4 Angstrom Crystal Structure of the Asymmetric Platinum Complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lu5 | ||||||
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Title | 2.4 Angstrom Crystal Structure of the Asymmetric Platinum Complex {Pt(ammine)(cyclohexylamine)}2+ Bound to a Dodecamer DNA Duplex | ||||||
Components |
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Keywords | DNA / platinum-DNA complex | ||||||
Function / homology | CIS-(AMMINE)(CYCLOHEXYLAMINE)PLATINUM(II) COMPLEX / DNA / DNA (> 10) Function and homology information | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Silverman, A.P. / Bu, W. / Cohen, S.M. / Lippard, S.J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: 2.4-A Crystal Structure of the Asymmetric Platinum Complex {Pt(ammine)(cyclohexylamine)}2+ Bound to a Dodecamer DNA Duplex Authors: Silverman, A.P. / Bu, W. / Cohen, S.M. / Lippard, S.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lu5.cif.gz | 36.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lu5.ent.gz | 24.5 KB | Display | PDB format |
PDBx/mmJSON format | 1lu5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lu/1lu5 ftp://data.pdbj.org/pub/pdb/validation_reports/lu/1lu5 | HTTPS FTP |
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-Related structure data
Related structure data | 1aioS 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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2 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 3565.316 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: DNA chain | Mass: 3761.468 Da / Num. of mol.: 2 / Source method: obtained synthetically #3: Chemical | #4: 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: 3.78 Å3/Da / Density % sol: 67.4 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: spermine, sodium cacodylate, magnesium acetate, PEG 4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 4. ℃ | ||||||||||||||||||||||||||||||||||||||||||
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: APS / Beamline: 19-ID / Wavelength: 0.97 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Aug 12, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 7337 / % possible obs: 96.3 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.082 / Rsym value: 0.09 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 2.4→2.49 Å / Rmerge(I) obs: 0.251 / Rsym value: 0.277 / % possible all: 96.3 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. measured all: 42245 / Rmerge(I) obs: 0.09 |
Reflection shell | *PLUS % possible obs: 96.3 % / Rmerge(I) obs: 0.277 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 1AIO Resolution: 2.4→50 Å / Num. parameters: 4163 / Num. restraintsaints: 4897 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 4 / σ(I): 2
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Refine analyze | Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1037 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→50 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 50 Å / Num. reflection obs: 5267 / Num. reflection Rfree: 565 / % reflection Rfree: 10 % / Rfactor all: 0.234 / Rfactor Rfree: 0.2495 / Rfactor Rwork: 0.2008 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: s_plane_restr / Dev ideal: 0.0003 |