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Yorodumi- PDB-195d: X-RAY STRUCTURES OF THE B-DNA DODECAMER D(CGCGTTAACGCG) WITH AN I... -
+Open data
-Basic information
Entry | Database: PDB / ID: 195d | ||||||||||||||||||
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Title | X-RAY STRUCTURES OF THE B-DNA DODECAMER D(CGCGTTAACGCG) WITH AN INVERTED CENTRAL TETRANUCLEOTIDE AND ITS NETROPSIN COMPLEX | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / B-DNA / DOUBLE HELIX / COMPLEXED WITH DRUG | Function / homology | NETROPSIN / DNA / DNA (> 10) | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 2.3 Å | Authors | Balendiran, K. / Rao, S.T. / Sekharudu, C.Y. / Zon, G. / Sundaralingam, M. | Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1995 | Title: X-ray structures of the B-DNA dodecamer d(CGCGTTAACGCG) with an inverted central tetranucleotide and its netropsin complex. Authors: Balendiran, K. / Rao, S.T. / Sekharudu, C.Y. / Zon, G. / Sundaralingam, M. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 195d.cif.gz | 26.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb195d.ent.gz | 16.6 KB | Display | PDB format |
PDBx/mmJSON format | 195d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/95/195d ftp://data.pdbj.org/pub/pdb/validation_reports/95/195d | HTTPS FTP |
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-Related structure data
-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 #2: Chemical | ChemComp-NT / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.37 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 282 K / Method: vapor diffusion / pH: 7.5 / Details: pH 7.50, VAPOR DIFFUSION, temperature 282.00K | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 282 K / pH: 7.5 / Method: vapor diffusion | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 258 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 |
Detector | Detector: AREA DETECTOR |
Radiation | Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Highest resolution: 2.3 Å / Num. obs: 2725 |
Reflection | *PLUS Highest resolution: 2.3 Å / Rmerge(I) obs: 0.051 |
-Processing
Software | Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.3→6 Å / σ(F): 2 /
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Refine Biso |
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Refinement step | Cycle: LAST / Resolution: 2.3→6 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 6 Å / σ(F): 2 / Rfactor obs: 0.162 / Rfactor Rwork: 0.162 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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