[English] 日本語
![](img/lk-miru.gif)
- PDB-7jvw: Crystal structure of human histone deacetylase 8 (HDAC8) G320R mu... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7jvw | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of human histone deacetylase 8 (HDAC8) G320R mutation complexed with M344 | ||||||
![]() | Histone deacetylase 8 | ||||||
![]() | HYDROLASE / Histone deacetylase / Cornelia de Lange Syndrome (CdLS) | ||||||
Function / homology | ![]() histone decrotonylase activity / histone deacetylase / protein lysine deacetylase activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / regulation of telomere maintenance / mitotic sister chromatid cohesion / histone deacetylase activity / nuclear chromosome / Notch-HLH transcription pathway / histone deacetylase complex ...histone decrotonylase activity / histone deacetylase / protein lysine deacetylase activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / regulation of telomere maintenance / mitotic sister chromatid cohesion / histone deacetylase activity / nuclear chromosome / Notch-HLH transcription pathway / histone deacetylase complex / negative regulation of protein ubiquitination / Resolution of Sister Chromatid Cohesion / Hsp70 protein binding / epigenetic regulation of gene expression / HDACs deacetylate histones / Hsp90 protein binding / regulation of protein stability / NOTCH1 Intracellular Domain Regulates Transcription / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Separation of Sister Chromatids / chromatin organization / DNA-binding transcription factor binding / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Osko, J.D. / Christianson, D.W. / Decroos, C. / Porter, N.J. / Lee, M. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Structural analysis of histone deacetylase 8 mutants associated with Cornelia de Lange Syndrome spectrum disorders. Authors: Osko, J.D. / Porter, N.J. / Decroos, C. / Lee, M.S. / Watson, P.R. / Raible, S.E. / Krantz, I.D. / Deardorff, M.A. / Christianson, D.W. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 187.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 117.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 7jvuC ![]() 7jvvC ![]() 3ewfS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||
2 | ![]()
| ||||||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 43332.137 Da / Num. of mol.: 2 / Mutation: G320R Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-K / #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.93 % |
---|---|
Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.3 / Details: 0.1 M MES, pH 5.3, 3% PEG1500, 4 mM TCEP |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 9, 2015 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→82.75 Å / Num. obs: 31564 / % possible obs: 97.4 % / Redundancy: 3.8 % / Biso Wilson estimate: 34.6910203953 Å2 / CC1/2: 0.981 / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.09 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.961 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 30670 / CC1/2: 0.578 / Rpim(I) all: 0.571 / % possible all: 96 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB entry 3EWF Resolution: 2.40301779656→48.9900201109 Å / SU ML: 0.381622707936 / Cross valid method: FREE R-VALUE / σ(F): 1.33674203891 / Phase error: 29.5397908894 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.6687983774 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.40301779656→48.9900201109 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|