+Open data
-Basic information
Entry | Database: PDB / ID: 1jtl | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | The crystal structure of d(GGCCAATTGG) Complexed with Distamycin | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA / B-DNA double helix / base triplets / minor groove binding / drug / distamycin | Function / homology | DISTAMYCIN A / DNA | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | Authors | Uytterhoeven, K. / Van Meervelt, L. | Citation | Journal: Eur.J.Biochem. / Year: 2002 | Title: Two 1 : 1 binding modes for distamycin in the minor groove of d(GGCCAATTGG). Authors: Uytterhoeven, K. / Sponer, J. / Van Meervelt, L. History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1jtl.cif.gz | 23.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1jtl.ent.gz | 14.8 KB | Display | PDB format |
PDBx/mmJSON format | 1jtl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jtl_validation.pdf.gz | 609.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1jtl_full_validation.pdf.gz | 614.7 KB | Display | |
Data in XML | 1jtl_validation.xml.gz | 4.8 KB | Display | |
Data in CIF | 1jtl_validation.cif.gz | 6.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jt/1jtl ftp://data.pdbj.org/pub/pdb/validation_reports/jt/1jtl | HTTPS FTP |
-Related structure data
Related structure data | 1k2zC C: citing same article (ref.) |
---|---|
Similar structure data | |
Other databases |
|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: DNA chain | Mass: 3085.029 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: This sequence is synthesized by Oswell DNA Service (Southampton, UK) #2: Chemical | ChemComp-DMY / | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35.32 % | ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: MPD, magnesium chloride, cacodylate, spermine, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
| ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 5 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8423 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 18, 2000 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8423 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→100 Å / Num. all: 4543 / Num. obs: 4223 / % possible obs: 93 % / Observed criterion σ(F): 2.5 / Observed criterion σ(I): 5 / Redundancy: 4.3 % / Biso Wilson estimate: 33.99 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 21.08 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 5.1 / Num. unique all: 431 / Rsym value: 0.195 / % possible all: 96.9 |
Reflection | *PLUS Num. measured all: 43223 / Rmerge(I) obs: 0.049 |
Reflection shell | *PLUS % possible obs: 96.9 % / Rmerge(I) obs: 0.195 |
-Processing
Software |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: DD0002 used as starting model for refinement Resolution: 1.85→100 Å / Isotropic thermal model: Isotropic / σ(F): 4 / Stereochemistry target values: user defined
| ||||||||||||
Displacement parameters | Biso mean: 33.99 Å2 | ||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→100 Å
| ||||||||||||
Refine LS restraints |
| ||||||||||||
Software | *PLUS Name: SHELXL / Version: 93 / Classification: refinement | ||||||||||||
Refinement | *PLUS Rfactor all: 0.2127 / Rfactor obs: 0.1974 / Rfactor Rfree: 0.278 / Rfactor Rwork: 0.1974 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS | ||||||||||||
Refine LS restraints | *PLUS
|