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- PDB-6pzo: Crystal structure of Danio rerio histone deacetylase 6 catalytic ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6pzo | ||||||
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Title | Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 complexed with YX-153 | ||||||
![]() | Hdac6 protein | ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / Histone deacetylase / metallohydrolase / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | ![]() 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 / angiogenesis / negative regulation of transcription by RNA polymerase II / zinc ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Osko, J.D. / Christianson, D.W. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Exploring Structural Determinants of Inhibitor Affinity and Selectivity in Complexes with Histone Deacetylase 6. Authors: Osko, J.D. / Porter, N.J. / Narayana Reddy, P.A. / Xiao, Y.C. / Rokka, J. / Jung, M. / Hooker, J.M. / Salvino, J.M. / Christianson, D.W. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 168.2 KB | Display | ![]() |
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PDB format | ![]() | 128.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 379.5 KB | Display | ![]() |
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Full document | ![]() | 379.9 KB | Display | |
Data in XML | ![]() | 2.1 KB | Display | |
Data in CIF | ![]() | 12.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6pzrC ![]() 6pzsC ![]() 6pzuC ![]() 6q0zC ![]() 5eemS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 39724.973 Da / Num. of mol.: 2 / Fragment: catalytic domain 2 (UNP residues 290-646) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: A7YT55, UniProt: F8W4B7*PLUS, histone deacetylase #2: Chemical | #3: Chemical | ChemComp-K / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.65 % / Description: thick plate-like crystals |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 10 mg/mL zCD2 protein, 2 mM YX-153 inhibitor, 0.2 M succinic acid, pH 7.0, 20% w/v PEG3350, 1:1 ratio protein to precipitant |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 31, 2018 |
Radiation | Monochromator: single crystal Si(220) side bounce / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→66.88 Å / Num. obs: 107228 / % possible obs: 99.7 % / Redundancy: 13.2 % / CC1/2: 0.994 / Rmerge(I) obs: 0.31 / Rpim(I) all: 0.088 / Net I/σ(I): 6.5 |
Reflection shell | Resolution: 1.5→1.55 Å / Rmerge(I) obs: 1.566 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 10523 / CC1/2: 0.998 / Rpim(I) all: 0.438 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB Entry 5EEM Resolution: 1.5→66.88 Å / Cross valid method: FREE R-VALUE /
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Refinement step | Cycle: LAST / Resolution: 1.5→66.88 Å
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