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Yorodumi- PDB-3vwd: Crystal structure of alpha-tubulin acetyltransferase domain of hu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vwd | ||||||
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Title | Crystal structure of alpha-tubulin acetyltransferase domain of human Mec-17 in complex with acetoacetyl-CoA (P21212 form) | ||||||
Components | Alpha-tubulin N-acetyltransferase | ||||||
Keywords | TRANSFERASE / GNAT fold / acetyltransferase | ||||||
Function / homology | Function and homology information alpha-tubulin N-acetyltransferase / tubulin N-acetyltransferase activity / alpha-tubulin acetylation / microtubule bundle / Cilium Assembly / NLRP3 inflammasome complex assembly / lysine N-acetyltransferase activity, acting on acetyl phosphate as donor / dentate gyrus development / regulation of fat cell differentiation / positive regulation of NLRP3 inflammasome complex assembly ...alpha-tubulin N-acetyltransferase / tubulin N-acetyltransferase activity / alpha-tubulin acetylation / microtubule bundle / Cilium Assembly / NLRP3 inflammasome complex assembly / lysine N-acetyltransferase activity, acting on acetyl phosphate as donor / dentate gyrus development / regulation of fat cell differentiation / positive regulation of NLRP3 inflammasome complex assembly / response to pain / cilium assembly / neuron development / regulation of microtubule cytoskeleton organization / response to mechanical stimulus / clathrin-coated pit / mitotic spindle / microtubule cytoskeleton organization / spermatogenesis / microtubule / axon / focal adhesion / Golgi apparatus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.25 Å | ||||||
Authors | Yuzawa, S. / Sumimoto, H. | ||||||
Citation | Journal: To be Published Title: Crystal structure of alpha-tubulin acetyltransferase domain of human Mec-17 Authors: Yuzawa, S. / Sumimoto, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vwd.cif.gz | 100 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vwd.ent.gz | 75.2 KB | Display | PDB format |
PDBx/mmJSON format | 3vwd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vw/3vwd ftp://data.pdbj.org/pub/pdb/validation_reports/vw/3vwd | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 22933.211 Da / Num. of mol.: 1 Fragment: alpha-tubulin acetyltransferase domain, UNP residues 1-194 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ATAT1, C6orf134, MEC17, Nbla00487 / Plasmid: pRSFDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q5SQI0, alpha-tubulin N-acetyltransferase | ||||
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#2: Chemical | ChemComp-ACO / | ||||
#3: Chemical | #4: Chemical | ChemComp-EDO / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.12 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M Bis-tris propane, 20% PEG 3350, 0.2M sodium formate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 17, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) channel-cut monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.25→50 Å / Num. obs: 54920 / % possible obs: 97.7 % / Redundancy: 12.6 % / Biso Wilson estimate: 9.94 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 11.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→35.808 Å / Occupancy max: 1 / Occupancy min: 0.39 / SU ML: 0.1 / σ(F): 1.35 / Phase error: 14.67 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.4301 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.25→35.808 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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