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- PDB-3f07: Crystal Structure Analysis of Human HDAC8 complexed with APHA in ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3f07 | ||||||
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Title | Crystal Structure Analysis of Human HDAC8 complexed with APHA in a new monoclinic crystal form | ||||||
![]() | Histone deacetylase 8 | ||||||
![]() | HYDROLASE / HDAC / metalloenzyme / acetylation / arginase fold / HDAC8 / histone deacetylase 8 / hydroxamate inhibitor / mutant / Alternative splicing / Chromatin regulator / Nucleus / Repressor / Transcription / Transcription regulation | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Dowling, D.P. / Gantt, S.L. / Gattis, S.G. / Fierke, C.A. / Christianson, D.W. | ||||||
![]() | ![]() Title: Structural studies of human histone deacetylase 8 and its site-specific variants complexed with substrate and inhibitors. Authors: Dowling, D.P. / Gantt, S.L. / Gattis, S.G. / Fierke, C.A. / Christianson, D.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 217.4 KB | Display | ![]() |
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PDB format | ![]() | 174 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3ew8C ![]() 3ewfC ![]() 3ezpC ![]() 3eztC ![]() 3f06C ![]() 3f0rC ![]() 1w22S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 43174.941 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-K / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.52 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.8 Details: Final drop concentrations of 25 mM Tris, 2.5% glycerol, 75 mM KCl, 1-5% PEG 6000, 50 mM MES, 1 mM tri(2-carboxyethyl)phosphine (TCEP), 0.03 mM gly-gly-gly, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 20, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0085 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→32 Å / Num. all: 21912 / Num. obs: 21912 / % possible obs: 98.8 % / Redundancy: 3.1 % / Biso Wilson estimate: 66.9 Å2 / Rmerge(I) obs: 0.136 / Net I/σ(I): 8 |
Reflection shell | Resolution: 3.3→3.42 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 3.2 / Num. unique all: 2212 / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1W22 Resolution: 3.3→31.5 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 63030.99 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 20.7651 Å2 / ksol: 0.3 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.3→31.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.3→3.51 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
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Xplor file |
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