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Yorodumi- PDB-455d: A6/A18 INTER-STRAND DITHIOBIS(PROPANE)-CROSSLINKED DODECAMER (CGC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 455d | ||||||||||||||||||
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Title | A6/A18 INTER-STRAND DITHIOBIS(PROPANE)-CROSSLINKED DODECAMER (CGCGAATTCGCG)2 | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / INTER-STRAND CROSSLINKING / DODECAMER CGCGAATTCGCG/CGCGAATTCGCG / DEOXYRIBONUCLEIC ACID | Function / homology | DITHIOBIS-(PROPANE) / DNA / DNA (> 10) | Function and homology information Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMEN / Resolution: 1.43 Å | Authors | Chiu, T.K. / Kaczor-Grzeskowiak, M. / Dickerson, R.E. | Citation | Journal: J.Mol.Biol. / Year: 1999 | Title: Absence of minor groove monovalent cations in the crosslinked dodecamer C-G-C-G-A-A-T-T-C-G-C-G. Authors: Chiu, T.K. / Kaczor-Grzeskowiak, M. / Dickerson, R.E. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 455d.cif.gz | 27.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb455d.ent.gz | 17.4 KB | Display | PDB format |
PDBx/mmJSON format | 455d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 455d_validation.pdf.gz | 382.2 KB | Display | wwPDB validaton report |
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Full document | 455d_full_validation.pdf.gz | 382.2 KB | Display | |
Data in XML | 455d_validation.xml.gz | 5.1 KB | Display | |
Data in CIF | 455d_validation.cif.gz | 6.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/55/455d ftp://data.pdbj.org/pub/pdb/validation_reports/55/455d | 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: 3663.392 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: COMPLEXED WITH THIOPROPANE #2: Chemical | #3: Chemical | ChemComp-SSP / | #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: 1.78 Å3/Da / Density % sol: 30.5 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.43→8 Å / Num. obs: 11200 / % possible obs: 89.4 % / Observed criterion σ(I): -3 / Redundancy: 9.49 % / Biso Wilson estimate: 17.85 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 38.1 |
Reflection shell | Resolution: 1.43→1.54 Å / Redundancy: 6.73 % / Rmerge(I) obs: 0.156 / Mean I/σ(I) obs: 10.9 / % possible all: 80.8 |
Reflection | *PLUS Lowest resolution: 8 Å / Observed criterion σ(I): 2 / Num. measured all: 106309 |
Reflection shell | *PLUS % possible obs: 80.8 % / Mean I/σ(I) obs: 10.93 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMEN Starting model: IDEAL B-DNA Resolution: 1.43→8 Å / Cross valid method: THROUGHOUT / σ(F): 2 Details: STARTING MODEL IS IDEAL B-DNA RMS-FITTED ONTO COORDINATES OF ORIGINAL DREW STRUCTURE (1BNA)
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Displacement parameters | Biso mean: 13.56 Å2
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Refinement step | Cycle: LAST / Resolution: 1.43→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.843 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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