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Yorodumi- PDB-335d: THE CRYSTAL STRUCTURE OF THE DNA DECAMER D(GGCAATTGCG) CONTAINS B... -
+Open data
-Basic information
Entry | Database: PDB / ID: 335d | ||||||||||||||||||
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Title | THE CRYSTAL STRUCTURE OF THE DNA DECAMER D(GGCAATTGCG) CONTAINS BOTH MAJOR AND MINOR GROOVE BINDING G.(G.C) TRIPLETS | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / A-DNA / DOUBLE HELIX / FLIPPED-OUT BASE | Function / homology | DNA | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 2.4 Å | Authors | Nunn, C.M. / Neidle, S. | Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1998 | Title: Structure of the DNA decamer d(GGCAATTGCG) contains both major- and minor-groove binding G.(G.C) base triplets. Authors: Nunn, C.M. / Neidle, S. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 335d.cif.gz | 17 KB | Display | PDBx/mmCIF format |
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PDB format | pdb335d.ent.gz | 10.1 KB | Display | PDB format |
PDBx/mmJSON format | 335d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 335d_validation.pdf.gz | 367 KB | Display | wwPDB validaton report |
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Full document | 335d_full_validation.pdf.gz | 370.1 KB | Display | |
Data in XML | 335d_validation.xml.gz | 3.9 KB | Display | |
Data in CIF | 335d_validation.cif.gz | 4.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/35/335d ftp://data.pdbj.org/pub/pdb/validation_reports/35/335d | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: DNA chain | Mass: 3085.029 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: Chemical | ChemComp-MG / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.56 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION, SITTING DROP | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 277 K / pH: 7 | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: ROTATING ANODE |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: May 22, 1996 / Details: MSC/YALE MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.4→8 Å / Num. obs: 1177 / % possible obs: 96 % / Rmerge(I) obs: 0.08 |
Reflection | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 8 Å / % possible obs: 96 % / Num. measured all: 1944 / Rmerge(I) obs: 0.08 |
-Processing
Software |
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Refinement | Starting model: PIECE OF UDJ031 Resolution: 2.4→8 Å / σ(F): 2
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Refine Biso |
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Refinement step | Cycle: LAST / Resolution: 2.4→8 Å
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Refine LS restraints |
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Xplor file | Serial no: 1 / Param file: NDB_TOPOLOGY_FILE.DNA / Topol file: NDB_PARAMETER_FILE.DNA | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 8 Å / σ(F): 2 / Rfactor obs: 0.195 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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