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Yorodumi- PDB-1d8g: ULTRAHIGH RESOLUTION CRYSTAL STRUCTURE OF B-DNA DECAMER D(CCAGTACTGG) -
+Open data
-Basic information
Entry | Database: PDB / ID: 1d8g | ||||||||||||||||||
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Title | ULTRAHIGH RESOLUTION CRYSTAL STRUCTURE OF B-DNA DECAMER D(CCAGTACTGG) | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA / B-DNA / ALTERNATE CONFORMATION / ULTRAHIGH RESOLUTION / TRP REPRESSOR / POLYAMIDE | Function / homology | DNA | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 0.74 Å | Authors | Kielkopf, C.L. / Ding, S. / Kuhn, P. / Rees, D.C. | Citation | Journal: J.Mol.Biol. / Year: 2000 | Title: Conformational flexibility of B-DNA at 0.74 A resolution: d(CCAGTACTGG)(2). Authors: Kielkopf, C.L. / Ding, S. / Kuhn, P. / Rees, D.C. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1d8g.cif.gz | 29.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1d8g.ent.gz | 19.1 KB | Display | PDB format |
PDBx/mmJSON format | 1d8g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1d8g_validation.pdf.gz | 378.9 KB | Display | wwPDB validaton report |
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Full document | 1d8g_full_validation.pdf.gz | 382.8 KB | Display | |
Data in XML | 1d8g_validation.xml.gz | 5.2 KB | Display | |
Data in CIF | 1d8g_validation.cif.gz | 6.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d8/1d8g ftp://data.pdbj.org/pub/pdb/validation_reports/d8/1d8g | 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 on special symmetry positions |
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-Components
#1: DNA chain | Mass: 3045.004 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
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#2: Chemical | ChemComp-CA / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.81 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 Details: MPD, CALCIUM ACETATE, TRIS(HYDROXYAMINOMETHANE) BUFFER, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K | |||||||||||||||||||||||||||||||||||
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 |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 0.74→16 Å / Num. all: 29991 / Num. obs: 29991 / % possible obs: 90 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 26.7 | ||||||||||||||||||||||||
Reflection shell | Resolution: 0.74→0.75 Å / Rmerge(I) obs: 0.239 / % possible all: 71.1 | ||||||||||||||||||||||||
Reflection | *PLUS Num. measured all: 130259 | ||||||||||||||||||||||||
Reflection shell | *PLUS % possible obs: 71.1 % / Mean I/σ(I) obs: 6.9 |
-Processing
Software |
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Refinement | Resolution: 0.74→16 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: SADI RESTRAINTS ON BACKBONE
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Refinement step | Cycle: LAST / Resolution: 0.74→16 Å
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 28208 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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