[English] 日本語
![](img/lk-miru.gif)
- PDB-8cok: Structural analysis of ING3 protein and its binding to histone H3 -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8cok | ||||||
---|---|---|---|---|---|---|---|
Title | Structural analysis of ING3 protein and its binding to histone H3 | ||||||
![]() | Inhibitor of growth protein 3 | ||||||
![]() | DNA BINDING PROTEIN / ING3 / histone H3 / PHD / protein structure / molecular recognition | ||||||
Function / homology | ![]() histone H2A acetyltransferase activity / : / : / : / histone H4K12 acetyltransferase activity / piccolo histone acetyltransferase complex / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H4K16 acetyltransferase activity / Swr1 complex ...histone H2A acetyltransferase activity / : / : / : / histone H4K12 acetyltransferase activity / piccolo histone acetyltransferase complex / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H4K16 acetyltransferase activity / Swr1 complex / NuA4 histone acetyltransferase complex / positive regulation of double-strand break repair via homologous recombination / methylated histone binding / nucleosome / chromatin organization / regulation of cell cycle / positive regulation of apoptotic process / regulation of DNA-templated transcription / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ferreras-Gutierrez, M. / Medrano, F.J. / Blanco, F.J. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Structural analysis of ING3 protein and histone H3 binding. Authors: Ferreras-Gutierrez, M. / Chaves-Arquero, B. / Gonzalez-Magana, A. / Merino, N. / Amusategui-Mateu, I. / Huecas, S. / Medrano, F.J. / Blanco, F.J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 113.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 78.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 7zmxC C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 12639.346 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.24 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: 0.1 M phosphate-citrate buffer at pH 4.2, 10 % 2-propanol and 0.2 M Li2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 16, 2022 / Details: KB focusing mirrors |
Radiation | Monochromator: Channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979257 Å / Relative weight: 1 |
Reflection | Resolution: 2.91→74.69 Å / Num. obs: 6277 / % possible obs: 95.7 % / Redundancy: 73.9 % / Biso Wilson estimate: 126.07 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.011 / Rrim(I) all: 0.081 / Net I/σ(I): 41.4 |
Reflection shell | Resolution: 2.91→3 Å / Redundancy: 80.3 % / Rmerge(I) obs: 6.609 / Num. unique obs: 319 / CC1/2: 0.565 / Rpim(I) all: 0.738 / Rrim(I) all: 6.651 / % possible all: 55.9 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 126.73 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.91→60.99 Å
| |||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||
LS refinement shell |
|