[English] 日本語
![](img/lk-miru.gif)
- PDB-5e8i: Crystal structure of the DNA binding domain of human transcriptio... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5e8i | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the DNA binding domain of human transcription factor FLI1 in complex with a 10-mer DNA ACCGGAAGTG | ||||||
![]() |
| ||||||
![]() | DNA BINDING PROTEIN/DNA / Transcription / DNA binding / Ewing sarcoma / Winged helix / ETS family / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | ![]() hemostasis / blood circulation / megakaryocyte development / animal organ morphogenesis / Transcriptional regulation of granulopoiesis / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / nuclear body / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific ...hemostasis / blood circulation / megakaryocyte development / animal organ morphogenesis / Transcriptional regulation of granulopoiesis / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / nuclear body / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / DNA binding / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hou, C. / Tsodikov, O.V. | ||||||
![]() | ![]() Title: Structural Basis for Dimerization and DNA Binding of Transcription Factor FLI1. Authors: Hou, C. / Tsodikov, O.V. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 136.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 100.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 466.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 466.6 KB | Display | |
Data in XML | ![]() | 15.6 KB | Display | |
Data in CIF | ![]() | 22.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5e8gC ![]() 4iriS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 14946.829 Da / Num. of mol.: 4 / Fragment: UNP residues 276-399 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: DNA chain | Mass: 3094.042 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) ![]() #3: DNA chain | Mass: 2995.967 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) ![]() #4: Chemical | ChemComp-CA / #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.97 Å3/Da / Density % sol: 58.52 % |
---|---|
Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M Na cacodylate pH 6.5, 0.2 M CaCl2, 14% w/v PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300HS / Detector: CCD / Date: Aug 5, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.45→50 Å / Num. obs: 13800 / % possible obs: 99.9 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 19 |
Reflection shell | Resolution: 3.45→3.51 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 1.9 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 4IRI Resolution: 3.45→35 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.933 / SU B: 37.095 / SU ML: 0.517 / Cross valid method: THROUGHOUT / ESU R Free: 0.577 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 133.671 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 3.45→35 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|