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Yorodumi- PDB-5wgl: Crystal structure of Danio rerio histone deacetylase 6 catalytic ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5wgl | ||||||
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Title | Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with ricolinostat (ACY-1215) | ||||||
Components | Hdac6 protein | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / histone deacetylase / hydrolase inhibitor / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information : / Aggrephagy / : / tubulin deacetylase activity / swimming behavior / definitive hemopoiesis / protein lysine deacetylase activity / histone deacetylase activity / regulation of tubulin deacetylation / potassium ion binding ...: / Aggrephagy / : / tubulin deacetylase activity / swimming behavior / definitive hemopoiesis / protein lysine deacetylase activity / histone deacetylase activity / regulation of tubulin deacetylation / potassium ion binding / histone deacetylase complex / hematopoietic progenitor cell differentiation / angiogenesis / negative regulation of transcription by RNA polymerase II / zinc ion binding Similarity search - Function | ||||||
Biological species | Danio rerio (zebrafish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Porter, N.J. / Christianson, D.W. | ||||||
Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017 Title: Unusual zinc-binding mode of HDAC6-selective hydroxamate inhibitors. Authors: Porter, N.J. / Mahendran, A. / Breslow, R. / 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 | 5wgl.cif.gz | 174.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wgl.ent.gz | 134.4 KB | Display | PDB format |
PDBx/mmJSON format | 5wgl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wg/5wgl ftp://data.pdbj.org/pub/pdb/validation_reports/wg/5wgl | HTTPS FTP |
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-Related structure data
Related structure data | 5wgiC 5wgkC 5wgmC 5eemS S: Starting model for refinement C: citing same article (ref.) |
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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 , 1 types, 2 molecules AB
#1: Protein | Mass: 40285.484 Da / Num. of mol.: 2 / Fragment: catalytic domain 2 (UNP residues 288-646) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Danio rerio (zebrafish) / Gene: hdac6 / Production host: Escherichia coli (E. coli) / References: UniProt: A7YT55, UniProt: F8W4B7*PLUS |
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-Non-polymers , 7 types, 575 molecules
#2: Chemical | #3: Chemical | ChemComp-K / #4: Chemical | #5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-PEG / | #7: Chemical | ChemComp-FLC / | #8: 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: 2.83 Å3/Da / Density % sol: 56.59 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: sodium citrate, pH 5.5, PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.00003 Å |
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Sep 20, 2016 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00003 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→49.3 Å / Num. obs: 101104 / % possible obs: 99.9 % / Redundancy: 6.9 % / Net I/σ(I): 14.1 |
Reflection shell | Highest resolution: 1.7 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 5EEM Resolution: 1.7→49.298 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.65
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→49.298 Å
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Refine LS restraints |
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LS refinement shell |
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