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Yorodumi- PDB-6uoc: Crystal structure of Danio rerio histone deacetylase 6 catalytic ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6uoc | ||||||
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Title | Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 1 (CD1) K330L mutant complexed with Givinostat | ||||||
Components | Histone deacetylase 6 | ||||||
Keywords | Hydrolase/Hydrolase Inhibitor / Histone Deacetylase / Hydrolase-Hydrolase Inhibitor complex | ||||||
Function / homology | Function and homology information Aggrephagy / tubulin deacetylase activity / swimming behavior / definitive hemopoiesis / protein lysine deacetylase activity / regulation of tubulin deacetylation / histone deacetylase activity / potassium ion binding / histone deacetylase complex / hematopoietic progenitor cell differentiation ...Aggrephagy / tubulin deacetylase activity / swimming behavior / definitive hemopoiesis / protein lysine deacetylase activity / regulation of tubulin deacetylation / histone deacetylase activity / potassium ion binding / histone deacetylase complex / hematopoietic progenitor cell differentiation / epigenetic regulation of gene expression / angiogenesis / zinc ion binding Similarity search - Function | ||||||
Biological species | Danio rerio (zebrafish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.40000794136 Å | ||||||
Authors | Osko, J.D. / Christianson, D.W. | ||||||
Funding support | United States, 1items
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Citation | Journal: Biochemistry / Year: 2019 Title: Structural Basis of Catalysis and Inhibition of HDAC6 CD1, the Enigmatic Catalytic Domain of Histone Deacetylase 6. Authors: Osko, J.D. / 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 | 6uoc.cif.gz | 123.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6uoc.ent.gz | 73.8 KB | Display | PDB format |
PDBx/mmJSON format | 6uoc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6uoc_validation.pdf.gz | 350.3 KB | Display | wwPDB validaton report |
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Full document | 6uoc_full_validation.pdf.gz | 350.2 KB | Display | |
Data in XML | 6uoc_validation.xml.gz | 1.8 KB | Display | |
Data in CIF | 6uoc_validation.cif.gz | 8.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uo/6uoc ftp://data.pdbj.org/pub/pdb/validation_reports/uo/6uoc | HTTPS FTP |
-Related structure data
Related structure data | 6uo2C 6uo3C 6uo4C 6uo5C 6uo7C 6uobC 5eefS 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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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 40278.570 Da / Num. of mol.: 1 / Mutation: K330L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Danio rerio (zebrafish) / Gene: hdac6 / Production host: Escherichia coli (E. coli) / References: UniProt: F8W4B7 |
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-Non-polymers , 5 types, 439 molecules
#2: Chemical | #3: Chemical | ChemComp-ZN / | #4: Chemical | #5: Chemical | ChemComp-QCM / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.53 Å3/Da / Density % sol: 51.31 % / Description: Thin/Thick Plate-Like Shape |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 10 mg/ml HDAC6 CD1 2 mM Inhibitor 0.2 M magnesium formate dihydrate 20% PEG 3350 1:1 ratio protein to precipitant |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.98 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 8, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→42.9476472842 Å / Num. obs: 80865 / % possible obs: 99.7 % / Redundancy: 6.5 % / Biso Wilson estimate: 11.016022672 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.04 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 1.4→1.45 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 5.6 / Num. unique obs: 7985 / CC1/2: 0.952 / Rpim(I) all: 0.15 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5EEF Resolution: 1.40000794136→42.9476472842 Å / SU ML: 0.095673127259 / Cross valid method: FREE R-VALUE / σ(F): 1.33792355939 / Phase error: 15.2008364571
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.2124829674 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.40000794136→42.9476472842 Å
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Refine LS restraints |
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LS refinement shell |
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