[English] 日本語
![](img/lk-miru.gif)
- PDB-1xjx: The crystal structures of the DNA binding sites of the RUNX1 tran... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1xjx | ||||||
---|---|---|---|---|---|---|---|
Title | The crystal structures of the DNA binding sites of the RUNX1 transcription factor | ||||||
![]() |
| ||||||
![]() | DNA / A-DNA / DOUBLE HELIX / OVERHANGING BASES / RUNX1 | ||||||
Function / homology | DNA![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Kitayner, M. / Rozenberg, H. / Rabinovich, D. / Shakked, Z. | ||||||
![]() | ![]() Title: Structures of the DNA-binding site of Runt-domain transcription regulators. Authors: Kitayner, M. / Rozenberg, H. / Rabinovich, D. / Shakked, Z. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 20.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 12.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 378.9 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 382.3 KB | Display | |
Data in XML | ![]() | 4.4 KB | Display | |
Data in CIF | ![]() | 5.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: DNA chain | Mass: 2722.784 Da / Num. of mol.: 1 / Source method: obtained synthetically |
---|---|
#2: DNA chain | Mass: 2740.812 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.83 Å3/Da / Density % sol: 32.92 % | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: MPD, magnesium chloride, sodium cacodylate acid, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
|
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() | |||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Details: OSMIC CONFOCAL MIRROR | |||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
| |||||||||
Reflection | Resolution: 1.7→18.4 Å / Num. obs: 4315 / % possible obs: 95.9 % / Redundancy: 3.3 % / Rsym value: 0.039 / Net I/σ(I): 39.3 | |||||||||
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 4.9 / Rsym value: 0.236 / % possible all: 78.4 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: FIBER A-DNA Resolution: 1.7→15 Å / Num. parameters: 1744 / Num. restraintsaints: 5767 / Cross valid method: THROUGHOUT / σ(F): 0 Stereochemistry target values: L.CLOWNEY ET AL.,J.AM.CHEM.SOC.118(1996)509-518, A.GELBIN ET AL.,J.AM.CHEM.SOC.118(1996)519-529, G.PARKINSON ET AL.,ACTA CRYST.D52(1996)57-64 Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56
| |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 432 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→15 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
|