[English] 日本語
Yorodumi- PDB-392d: STRUCTURAL VARIABILITY AND NEW INTERMOLECULAR INTERACTIONS OF Z-D... -
+Open data
-Basic information
Entry | Database: PDB / ID: 392d | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | STRUCTURAL VARIABILITY AND NEW INTERMOLECULAR INTERACTIONS OF Z-DNA IN CRYSTALS OF D(PCPGPCPGPCPG) | ||||||||||||||||||
Components | DNA (5'-D(P*Keywords | DNA / Z-DNA / DOUBLE HELIX | Function / homology | DNA | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 3 Å | Authors | Malinina, L. / Tereshko, V. / Ivanova, E. / Subirana, J.A. / Zarytova, V. / Nekrasov, Y. | Citation | Journal: Biophys.J. / Year: 1998 Title: Structural variability and new intermolecular interactions of Z-DNA in crystals of d(pCpGpCpGpCpG). Authors: Malinina, L. / Tereshko, V. / Ivanova, E. / Subirana, J.A. / Zarytova, V. / Nekrasov, Y. #1: Journal: J.Biomol.Struct.Dyn. / Year: 1994 Title: A Simplified Multidimensional Search Used for Crystal Structure Sloution of pCpGpCpGpCpG with Two Duplexes per Asymmetric Unit Authors: Strocopytov, B.V. / Malinina, L.V. History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 392d.cif.gz | 18.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb392d.ent.gz | 12.2 KB | Display | PDB format |
PDBx/mmJSON format | 392d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 392d_validation.pdf.gz | 370 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 392d_full_validation.pdf.gz | 370 KB | Display | |
Data in XML | 392d_validation.xml.gz | 2.4 KB | Display | |
Data in CIF | 392d_validation.cif.gz | 2.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/92/392d ftp://data.pdbj.org/pub/pdb/validation_reports/92/392d | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: DNA chain | Mass: 1810.205 Da / Num. of mol.: 4 / Source method: obtained synthetically #2: Chemical | ChemComp-MG / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.67 % | ||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 6 / Details: pH 6.00 | ||||||||||||||||||||||||||||||||
Components of the solutions |
| ||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: other / Details: Malinina, L., (1991) J. Crystal Growth, 110, 252. | ||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 290 K |
---|---|
Diffraction source | Source: SEALED TUBE / Type: OTHER / Wavelength: 1.5418 |
Detector | Type: SYNTEX P21 / Detector: DIFFRACTOMETER / Date: Jan 1, 1988 |
Radiation | Monochromator: GRAPHITE / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3→35.2 Å / Num. obs: 1276 / % possible obs: 97.9 % / Observed criterion σ(I): 1 / Redundancy: 2 % / Rmerge(I) obs: 0.08 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 3→8 Å / Cross valid method: FREE R-VALUE / σ(F): 2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|