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Yorodumi- PDB-312d: Z-DNA HEXAMER WITH 5' OVERHANGS THAT FORM A REVERSE WATSON-CRICK ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 312d | ||||||
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Title | Z-DNA HEXAMER WITH 5' OVERHANGS THAT FORM A REVERSE WATSON-CRICK BASE PAIR | ||||||
Components |
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Keywords | DNA / Z-DNA / DOUBLE HELIX / OVERHANGING BASE / FLIPPED-OUT BASE | ||||||
Function / homology | COBALT HEXAMMINE(III) / DNA Function and homology information | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Mooers, B.H.M. / Eichman, B.F. / Ho, P.S. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1997 Title: The structures and relative stabilities of d(G x G) reverse Hoogsteen, d(G x T) reverse wobble, and d(G x C) reverse Watson-Crick base-pairs in DNA crystals. Authors: Mooers, B.H. / Eichman, B.F. / Ho, P.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 312d.cif.gz | 17.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb312d.ent.gz | 11.1 KB | Display | PDB format |
PDBx/mmJSON format | 312d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/12/312d ftp://data.pdbj.org/pub/pdb/validation_reports/12/312d | 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: 2139.411 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 2099.387 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-NCO / |
#5: 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: 1.84 Å3/Da / Density % sol: 32.98 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION, SITTING DROP / Temp details: ROOM TEMPERATURE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS pH: 7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SEALED TUBE / Wavelength: 1.5418 |
Detector | Type: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: May 1, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.48→14.2 Å / Num. obs: 5340 / % possible obs: 84.5 % / Observed criterion σ(I): 2 / Rsym value: 0.083 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 1.48→14.2 Å / Mean I/σ(I) obs: 3.37 / Rsym value: 0.433 |
Reflection | *PLUS Highest resolution: 1.48 Å / Lowest resolution: 14.2 Å / % possible obs: 84.5 % / Num. measured all: 20832 / Rmerge(I) obs: 0.083 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: ZDGB55 Resolution: 1.8→8 Å / σ(F): 3
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Displacement parameters | Biso mean: 13.33 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.88 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 8 Å / σ(F): 3 / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS % reflection Rfree: 1.2 % |