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Yorodumi- PDB-1dvl: CRYSTAL STRUCTURE OF THE 1:1 NETROPSIN-DECAMER D(CCIICICCII)2 COM... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dvl | ||||||||||||||||||
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Title | CRYSTAL STRUCTURE OF THE 1:1 NETROPSIN-DECAMER D(CCIICICCII)2 COMPLEX WITH ONLY ONE DRUG BOUND AT ONE END | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA / DRUG BINDING | Function / homology | NETROPSIN / DNA | Function and homology information Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | Authors | Shi, K. / Mitra, S.N. / Sundaralingam, M. | Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2002 | Title: Structure of the 1:1 netropsin-decamer d(CCIICICCII)2 complex with a single bound netropsin. Authors: Shi, K. / Mitra, S.N. / Sundaralingam, M. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dvl.cif.gz | 17.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dvl.ent.gz | 12.8 KB | Display | PDB format |
PDBx/mmJSON format | 1dvl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dv/1dvl ftp://data.pdbj.org/pub/pdb/validation_reports/dv/1dvl | 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: 2971.911 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Chemical | ChemComp-NT / | #3: 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: 2.08 Å3/Da / Density % sol: 40.81 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 4 MM DNA (SINGLE STRAND), 0.008M MGCL2, 0.04 M NA CACODYLATE (PH 6.5), 2MM NETROPSIN, VAPOR DIFFUSION, HANGING DROP at 293K | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 2.4 Å / Num. obs: 1795 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.037 |
Reflection shell | Resolution: 2.4→2.5 Å |
Reflection | *PLUS Highest resolution: 2.4 Å / Rmerge(I) obs: 0.037 |
Reflection shell | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 2.5 Å / % possible obs: 62.7 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→8 Å / Cross valid method: THROUGHOUT / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2.4→8 Å
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Refine LS restraints |
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Refinement | *PLUS % reflection Rfree: 10 % / Rfactor obs: 0.196 / Rfactor Rfree: 0.245 / Rfactor Rwork: 0.196 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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