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Yorodumi- PDB-210d: CRYSTAL AND MOLECULAR STRUCTURE OF A NEW Z-DNA CRYSTAL FORM: D[CG... -
+Open data
-Basic information
Entry | Database: PDB / ID: 210d | ||||||||||||||||||
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Title | CRYSTAL AND MOLECULAR STRUCTURE OF A NEW Z-DNA CRYSTAL FORM: D[CGT(2-NH2-A)CG] AND ITS PLATINATED DERIVATIVE | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / Z-DNA / DOUBLE HELIX / MODIFIED | Function / homology | SPERMINE / DNA | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 1.35 Å | Authors | Parkinson, G.N. / Arvantis, G.M. / Lessinger, L. / Ginell, S.L. / Jones, R. / Gaffney, B. / Berman, H.M. | Citation | Journal: Biochemistry / Year: 1995 | Title: Crystal and molecular structure of a new Z-DNA crystal form: d[CGT(2-NH2-A)CG] and its platinated derivative. Authors: Parkinson, G.N. / Arvanitis, G.M. / Lessinger, L. / Ginell, S.L. / Jones, R. / Gaffney, B. / Berman, H.M. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 210d.cif.gz | 13.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb210d.ent.gz | 7.3 KB | Display | PDB format |
PDBx/mmJSON format | 210d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 210d_validation.pdf.gz | 350.8 KB | Display | wwPDB validaton report |
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Full document | 210d_full_validation.pdf.gz | 350.8 KB | Display | |
Data in XML | 210d_validation.xml.gz | 2.3 KB | Display | |
Data in CIF | 210d_validation.cif.gz | 2.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/10/210d ftp://data.pdbj.org/pub/pdb/validation_reports/10/210d | HTTPS FTP |
-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: 1824.231 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: Chemical | ChemComp-SPM / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.91 Å3/Da / Density meas: 1.45 Mg/m3 / Density % sol: 35.5 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, sitting drop / Details: VAPOR DIFFUSION, SITTING DROP / Temp details: ROOM TEMPERATURE | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 291 K |
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Diffraction source | Source: ROTATING ANODE |
Detector | Type: ENRAF-NONIUS CAD4 / Detector: DIFFRACTOMETER |
Radiation | Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Highest resolution: 1.35 Å / Num. all: 4487 / Num. obs: 3408 / Observed criterion σ(F): 2 |
Reflection | *PLUS Highest resolution: 1.35 Å / Lowest resolution: 2.1 Å / Num. obs: 3408 / % possible obs: 94 % / Observed criterion σ(F): 4 / Num. measured all: 4487 |
Reflection shell | *PLUS Highest resolution: 1.35 Å / Lowest resolution: 1.5 Å / % possible obs: 53 % |
-Processing
Software | Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.35→12 Å / σ(F): 4
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Refinement step | Cycle: LAST / Resolution: 1.35→12 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 1.35 Å / Lowest resolution: 12 Å / σ(F): 4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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