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Yorodumi- PDB-8bjk: X-ray structure of Danio rerio histone deacetylase 6 (HDAC6) CD2 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8bjk | ||||||
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Title | X-ray structure of Danio rerio histone deacetylase 6 (HDAC6) CD2 in complex with an inhibitor CPD11352 | ||||||
Components | Histone deacetylase 6HDAC6 | ||||||
Keywords | HYDROLASE / HISTONE DEACETYLASE / DEACETYLATION / INHIBITOR / DANIO RERIO | ||||||
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 / FOURIER SYNTHESIS / Resolution: 1.35 Å | ||||||
Authors | Barinka, C. / Motlova, L. / Pavlicek, J. | ||||||
Funding support | 1items
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Citation | Journal: Acs Chem.Biol. / Year: 2023 Title: Comprehensive Mechanistic View of the Hydrolysis of Oxadiazole-Based Inhibitors by Histone Deacetylase 6 (HDAC6). Authors: Motlova, L. / Snajdr, I. / Kutil, Z. / Andris, E. / Ptacek, J. / Novotna, A. / Novakova, Z. / Havlinova, B. / Tueckmantel, W. / Draberova, H. / Majer, P. / Schutkowski, M. / Kozikowski, A. / ...Authors: Motlova, L. / Snajdr, I. / Kutil, Z. / Andris, E. / Ptacek, J. / Novotna, A. / Novakova, Z. / Havlinova, B. / Tueckmantel, W. / Draberova, H. / Majer, P. / Schutkowski, M. / Kozikowski, A. / Rulisek, L. / Barinka, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8bjk.cif.gz | 172 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8bjk.ent.gz | 132.1 KB | Display | PDB format |
PDBx/mmJSON format | 8bjk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bj/8bjk ftp://data.pdbj.org/pub/pdb/validation_reports/bj/8bjk | HTTPS FTP |
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-Related structure data
Related structure data | 6r0kS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 39899.125 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Danio rerio (zebrafish) / Gene: hdac6 / Cell line (production host): HEK293T / Organ (production host): kidney / Production host: Homo sapiens (human) / References: UniProt: F8W4B7 | ||||||
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#2: Chemical | ChemComp-ZN / | ||||||
#3: Chemical | #4: Chemical | ChemComp-QXF / ~{ | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.76 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 19% PEG 3350 (SIGMA-ALDRICH), 0.2 M KSCN (HAMPTON RESEARCH), 0.1 M BIS-TRIS Ph 6.5 (SIGMA-ALDRICH) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1.34 Å |
Detector | Type: Bruker PHOTON II / Detector: PIXEL / Date: Mar 5, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.34 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→62.64 Å / Num. obs: 90048 / % possible obs: 99.9 % / Redundancy: 15 % / CC1/2: 0.999 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.032 / Rrim(I) all: 0.125 / Net I/σ(I): 17.9 |
Reflection shell | Resolution: 1.35→1.37 Å / Mean I/σ(I) obs: 0.7 / Num. unique obs: 4356 / CC1/2: 0.3 / Rpim(I) all: 0.923 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 6r0k Resolution: 1.35→62.64 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.446 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.055 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.072 Å2
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Refinement step | Cycle: 1 / Resolution: 1.35→62.64 Å
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