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- PDB-5d1d: Crystal structure of P91L-Y306F HDAC8 in complex with a tetrapept... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5d1d | |||||||||
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Title | Crystal structure of P91L-Y306F HDAC8 in complex with a tetrapeptide substrate | |||||||||
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![]() | HYDROLASE / histone deacetylase / arginase/deacetylase fold / enzyme substrate complex | |||||||||
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 | ![]() unidentified (others) | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Decroos, C. / Christianson, N.H. / Gullett, L.E. / Bowman, C.M. / Christianson, K.E. / Deardorff, M.A. / Christianson, D.W. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Biochemical and Structural Characterization of HDAC8 Mutants Associated with Cornelia de Lange Syndrome Spectrum Disorders. Authors: Decroos, C. / Christianson, N.H. / Gullett, L.E. / Bowman, C.M. / Christianson, K.E. / Deardorff, M.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 | ![]() | 164.1 KB | Display | ![]() |
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PDB format | ![]() | 125.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5d1bC ![]() 5d1cC ![]() 3ewfS 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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Unit cell |
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Components
#1: Protein | Mass: 43232.035 Da / Num. of mol.: 2 / Mutation: P91L Y306F Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | Mass: 836.980 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) unidentified (others) #3: Chemical | #4: Chemical | ChemComp-K / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.23 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 100 mM Tris (pH 8.0), 10% (w/v) PEG 35000, 4 mM TCEP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 23, 2014 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 2.01→44.5 Å / Num. obs: 57560 / % possible obs: 99.9 % / Redundancy: 9.5 % / Rmerge(I) obs: 0.135 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 2.01→2.08 Å / Redundancy: 9.1 % / Rmerge(I) obs: 1.153 / Mean I/σ(I) obs: 2.1 / % possible all: 98.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3EWF Resolution: 2.011→44.5 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.13 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.011→44.5 Å
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Refine LS restraints |
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LS refinement shell |
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