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Yorodumi- PDB-2dbe: CRYSTAL STRUCTURE OF A BERENIL-DODECANUCLEOTIDE COMPLEX: THE ROLE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dbe | ||||||||||||||||||
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Title | CRYSTAL STRUCTURE OF A BERENIL-DODECANUCLEOTIDE COMPLEX: THE ROLE OF WATER IN SEQUENCE-SPECIFIC LIGAND BINDING | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / B-DNA / DOUBLE HELIX / COMPLEXED WITH DRUG | Function / homology | BERENIL / DNA / DNA (> 10) | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 2.5 Å | Authors | Brown, D.G. / Sanderson, M.R. / Skelly, J.V. / Jenkins, T.C. / Brown, T. / Garman, E. / Stuart, D.I. / Neidle, S. | Citation | Journal: EMBO J. / Year: 1990 | Title: Crystal structure of a berenil-dodecanucleotide complex: the role of water in sequence-specific ligand binding. Authors: Brown, D.G. / Sanderson, M.R. / Skelly, J.V. / Jenkins, T.C. / Brown, T. / Garman, E. / Stuart, D.I. / Neidle, S. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dbe.cif.gz | 24 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dbe.ent.gz | 15.2 KB | Display | PDB format |
PDBx/mmJSON format | 2dbe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2dbe_validation.pdf.gz | 388.6 KB | Display | wwPDB validaton report |
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Full document | 2dbe_full_validation.pdf.gz | 396.7 KB | Display | |
Data in XML | 2dbe_validation.xml.gz | 2.7 KB | Display | |
Data in CIF | 2dbe_validation.cif.gz | 3.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/db/2dbe ftp://data.pdbj.org/pub/pdb/validation_reports/db/2dbe | 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 #2: Chemical | ChemComp-BRN / | #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: 2.21 Å3/Da / Density % sol: 44.46 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 278 K / Method: vapor diffusion / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION, temperature 278.00K | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 278 K / pH: 7 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 |
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Detector | Type: XENTRONICS / Detector: AREA DETECTOR |
Radiation | Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Highest resolution: 2.5 Å / Num. all: 2195 / Num. obs: 1759 / Observed criterion σ(F): 2 / Rmerge(I) obs: 0.037 |
Reflection | *PLUS Highest resolution: 2.5 Å / Num. obs: 2195 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.037 / Num. measured all: 5762 |
-Processing
Software |
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Refinement | Highest resolution: 2.5 Å / σ(F): 2 /
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Refine Biso |
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Refinement step | Cycle: LAST / Highest resolution: 2.5 Å
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Refinement | *PLUS Highest resolution: 2.5 Å / σ(I): 2 / Rfactor obs: 0.167 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS Biso mean: 32 Å2 |