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Yorodumi- PDB-6cw8: Crystal structure of Danio rerio histone deacetylase 6 catalytic ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6cw8 | ||||||
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Title | Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 complexed with RTS-V5 | ||||||
Components | Hdac6 protein | ||||||
Keywords | HYDROLASE / Histone deacetylase / metallohydrolase | ||||||
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 / 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: 1.9 Å | ||||||
Authors | Osko, J.D. / Christianson, D.W. | ||||||
Funding support | United States, 1items
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Citation | Journal: J. Med. Chem. / Year: 2018 Title: Discovery of the First-in-Class Dual Histone Deacetylase-Proteasome Inhibitor. Authors: Bhatia, S. / Krieger, V. / Groll, M. / Osko, J.D. / Ahlert, H. / Borkhardt, A. / Kurz, T. / Christianson, D.W. / Hauer, J. / Hansen, F.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6cw8.cif.gz | 170.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6cw8.ent.gz | 130.8 KB | Display | PDB format |
PDBx/mmJSON format | 6cw8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6cw8_validation.pdf.gz | 999.9 KB | Display | wwPDB validaton report |
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Full document | 6cw8_full_validation.pdf.gz | 1003.1 KB | Display | |
Data in XML | 6cw8_validation.xml.gz | 31.3 KB | Display | |
Data in CIF | 6cw8_validation.cif.gz | 46.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cw/6cw8 ftp://data.pdbj.org/pub/pdb/validation_reports/cw/6cw8 | HTTPS FTP |
-Related structure data
Related structure data | 6h39C 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: 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 , 5 types, 536 molecules
#2: Chemical | #3: Chemical | ChemComp-K / #4: Chemical | #5: Chemical | ChemComp-EDO / #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: 2.32 Å3/Da / Density % sol: 47 % / Description: Long thick needle-like crystals |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 10 mg/mL ZCD2 1:1 drop ratio of protein to precipitant 0.2M lithium chloride, 20% w/v Polyethylene glycol (PEG) 3350 Crystals appeared within 2-3 days |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 20, 2017 |
Radiation | Monochromator: Dual Crystal Monochromator, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→64.21 Å / Num. obs: 64520 / % possible obs: 100 % / Redundancy: 8.8 % / CC1/2: 0.977 / Rmerge(I) obs: 0.35 / Rpim(I) all: 0.124 / Rrim(I) all: 0.372 / Net I/σ(I): 7 |
Reflection shell | Resolution: 1.9→1.94 Å / Redundancy: 7.8 % / Rmerge(I) obs: 1.584 / Num. unique obs: 4092 / CC1/2: 0.656 / Rpim(I) all: 0.592 / Rrim(I) all: 1.694 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 5EEM Resolution: 1.9→45.724 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.05
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→45.724 Å
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Refine LS restraints |
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LS refinement shell |
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