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Yorodumi- PDB-5eem: Crystal structure of Danio rerio histone deacetylase 6 catalytic ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5eem | ||||||
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Title | Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 | ||||||
Components | Hdac6 protein | ||||||
Keywords | HYDROLASE | ||||||
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: 2 Å | ||||||
Authors | Hai, Y. / Christianson, D.W. | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2016 Title: Histone deacetylase 6 structure and molecular basis of catalysis and inhibition. Authors: Hai, Y. / 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 | 5eem.cif.gz | 286.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5eem.ent.gz | 230.2 KB | Display | PDB format |
PDBx/mmJSON format | 5eem.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ee/5eem ftp://data.pdbj.org/pub/pdb/validation_reports/ee/5eem | HTTPS FTP |
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-Related structure data
Related structure data | 5eduC 5eefC 5eeiC 5eekSC 5eenC 5ef7C 5ef8C 5efbC 5efgC 5efhC 5efjC 5efkC 5efnC 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 , 1 types, 2 molecules BA
#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, histone deacetylase |
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-Non-polymers , 5 types, 315 molecules
#2: Chemical | #3: Chemical | ChemComp-K / #4: Chemical | ChemComp-NA / | #5: Chemical | ChemComp-FMT / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.69 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.1 M sodium acetate, 0.1 M sodium formate, 20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 15, 2015 |
Radiation | Monochromator: single crystal Si(220) side bounce / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 47957 / % possible obs: 97 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.162 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 2→2.15 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.501 / Mean I/σ(I) obs: 1.8 / % possible all: 96.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 5EEK Resolution: 2→15.91 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 29.19 / 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→15.91 Å
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Refine LS restraints |
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LS refinement shell |
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