+Open data
-Basic information
Entry | Database: PDB / ID: 5tht | ||||||
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Title | Crystal Structure of G303A HDAC8 in complex with M344 | ||||||
Components | Histone deacetylase 8 | ||||||
Keywords | HYDROLASE / Zinc Histone Deacetylase | ||||||
Function / homology | Function and homology information histone decrotonylase activity / histone deacetylase / protein lysine deacetylase activity / regulation of telomere maintenance / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / histone deacetylase activity / mitotic sister chromatid cohesion / nuclear chromosome / Notch-HLH transcription pathway / histone deacetylase complex ...histone decrotonylase activity / histone deacetylase / protein lysine deacetylase activity / regulation of telomere maintenance / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / histone deacetylase activity / mitotic sister chromatid cohesion / nuclear chromosome / Notch-HLH transcription pathway / histone deacetylase complex / negative regulation of protein ubiquitination / Hsp70 protein binding / Resolution of Sister Chromatid Cohesion / 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 / metal ion binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.407 Å | ||||||
Authors | Porter, N.J. / Christianson, D.W. | ||||||
Funding support | United States, 1items
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Citation | Journal: Biochemistry / Year: 2016 Title: Structural and Functional Influence of the Glycine-Rich Loop G302GGGY on the Catalytic Tyrosine of Histone Deacetylase 8. Authors: Porter, N.J. / Christianson, N.H. / Decroos, C. / Christianson, D.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5tht.cif.gz | 296.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5tht.ent.gz | 237.7 KB | Display | PDB format |
PDBx/mmJSON format | 5tht.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/th/5tht ftp://data.pdbj.org/pub/pdb/validation_reports/th/5tht | HTTPS FTP |
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-Related structure data
Related structure data | 5thsC 5thuC 5thvC 3ewfS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 43246.020 Da / Num. of mol.: 4 / Mutation: G303A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HDAC8, HDACL1, CDA07 / Plasmid: pET20b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q9BY41, histone deacetylase |
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-Non-polymers , 5 types, 253 molecules
#2: Chemical | ChemComp-B3N / #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-K / #5: Chemical | ChemComp-EDO / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.89 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / Details: 100 mM HEPES (pH 7.5), 22% w/v PEG 6000, 4 mM TCEP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97923 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 9, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97923 Å / Relative weight: 1 |
Reflection | Resolution: 2.407→97.66 Å / Num. obs: 62588 / % possible obs: 99.9 % / Redundancy: 3.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.068 / Rsym value: 0.066 / Net I/σ(I): 12.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3EWF Resolution: 2.407→97.656 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.06
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.407→97.656 Å
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Refine LS restraints |
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LS refinement shell |
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