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Yorodumi- PDB-5dc8: Crystal structure of H142A-Y306F HDAC8 in complex with a tetrapep... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5dc8 | |||||||||
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Title | Crystal structure of H142A-Y306F HDAC8 in complex with a tetrapeptide substrate | |||||||||
Components |
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Keywords | HYDROLASE / histone deacetylase 8 / arginase fold / deacetylase / enzyme-substrate complex | |||||||||
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 / 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 / regulation of telomere maintenance / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / 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 / 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 | Homo sapiens (human) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | |||||||||
Authors | Decroos, C. / Lee, M.S. / Christianson, D.W. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Biochemistry / Year: 2016 Title: General Base-General Acid Catalysis in Human Histone Deacetylase 8. Authors: Gantt, S.M. / Decroos, C. / Lee, M.S. / Gullett, L.E. / Bowman, C.M. / Christianson, D.W. / Fierke, C.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5dc8.cif.gz | 348.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dc8.ent.gz | 282.6 KB | Display | PDB format |
PDBx/mmJSON format | 5dc8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5dc8_validation.pdf.gz | 456.8 KB | Display | wwPDB validaton report |
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Full document | 5dc8_full_validation.pdf.gz | 460.2 KB | Display | |
Data in XML | 5dc8_validation.xml.gz | 37.3 KB | Display | |
Data in CIF | 5dc8_validation.cif.gz | 58.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dc/5dc8 ftp://data.pdbj.org/pub/pdb/validation_reports/dc/5dc8 | HTTPS FTP |
-Related structure data
Related structure data | 5dc5C 5dc6C 5dc7C 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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1 |
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2 |
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Unit cell |
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-Components
-Protein / Protein/peptide , 2 types, 4 molecules ABCD
#1: Protein | Mass: 43148.926 Da / Num. of mol.: 2 / Mutation: H142A, Y306F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HDAC8, HDACL1, CDA07 / Plasmid: pHD2-Xa-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9BY41, histone deacetylase #2: Protein/peptide | Mass: 836.980 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Non-polymers , 4 types, 838 molecules
#3: Chemical | #4: Chemical | ChemComp-K / #5: Chemical | #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: 2.41 Å3/Da / Density % sol: 48.95 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 100 mM Tris (pH 8.0), 10% (w/v) PEG 35000, and 4 mM TCEP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 20, 2015 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→49 Å / Num. obs: 208317 / % possible obs: 100 % / Redundancy: 7 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 1.3→1.35 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.855 / Mean I/σ(I) obs: 2.7 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3EWF Resolution: 1.3→49 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 12.8 / 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: 1.3→49 Å
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Refine LS restraints |
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LS refinement shell |
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