+Open data
-Basic information
Entry | Database: PDB / ID: 417d | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | A THYMINE-LIKE BASE ANALOGUE FORMS WOBBLE PAIRS WITH ADENINE | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / P.A BASE-PAIRS / PYRIMIDINE ANALOGUE / Z-DNA | Function / homology | DNA | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | Authors | Lin, P.K.T. / Schuerman, M.H. / Moore, G.S. / Van Meervelt, L. / Loakes, D. / Brown, D.M. / Moore, M.H. | Citation | Journal: J.Mol.Biol. / Year: 1998 | Title: A thymine-like base analogue forms wobble pairs with adenine in a Z-DNA duplex. Authors: Schuerman, G.S. / Van Meervelt, L. / Loakes, D. / Brown, D.M. / Kong Thoo Lin, P. / Moore, M.H. / Salisbury, S.A. History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 417d.cif.gz | 17.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb417d.ent.gz | 10.4 KB | Display | PDB format |
PDBx/mmJSON format | 417d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/17/417d ftp://data.pdbj.org/pub/pdb/validation_reports/17/417d | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
Unit cell |
|
-Components
#1: DNA chain | Mass: 1836.243 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.65 Å3/Da / Density % sol: 35 % | |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: CRYSTALS WERE OBTAINED FROM A SOLUTION THAT CONTAINED NA CACODYLATE, MG CHLORIDE, SPERMINE, MPD., pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 277.00K | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
| |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 6.5 | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 150 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 19, 1995 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.53→10 Å / Num. all: 3920 / Num. obs: 3920 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 21.08 |
Reflection shell | Resolution: 1.53→1.56 Å / Rmerge(I) obs: 0.104 / Mean I/σ(I) obs: 11.92 / % possible all: 92.5 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Resolution: 1.5→10 Å / Num. parameters: 2724 / Num. restraintsaints: 5294 / σ(F): 4 / Stereochemistry target values: SHELXL
| |||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: BABINET'S PRINCIPLE | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→10 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||
Software | *PLUS Name: SHELXL-93 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.5 Å / Lowest resolution: 10 Å / σ(F): 4 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |