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Yorodumi- PDB-6p12: Structure of spastin AAA domain (wild-type) in complex with diami... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6p12 | |||||||||
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Title | Structure of spastin AAA domain (wild-type) in complex with diaminotriazole-based inhibitor | |||||||||
Components | Drosophila melanogaster Spastin AAA domain | |||||||||
Keywords | ISOMERASE/ISOMERASE INHIBITOR / inhibitor / complex / AAA protein / ISOMERASE-ISOMERASE INHIBITOR complex | |||||||||
Function / homology | Function and homology information positive regulation of axon extension involved in regeneration / hemocyte migration / negative regulation of synaptic assembly at neuromuscular junction / Sealing of the nuclear envelope (NE) by ESCRT-III / negative regulation of neuromuscular synaptic transmission / positive regulation of neuromuscular synaptic transmission / microtubule-severing ATPase / positive regulation of synaptic assembly at neuromuscular junction / microtubule severing ATPase activity / mitotic chromosome movement towards spindle pole ...positive regulation of axon extension involved in regeneration / hemocyte migration / negative regulation of synaptic assembly at neuromuscular junction / Sealing of the nuclear envelope (NE) by ESCRT-III / negative regulation of neuromuscular synaptic transmission / positive regulation of neuromuscular synaptic transmission / microtubule-severing ATPase / positive regulation of synaptic assembly at neuromuscular junction / microtubule severing ATPase activity / mitotic chromosome movement towards spindle pole / microtubule severing / regulation of terminal button organization / positive regulation of lipid metabolic process / positive regulation of microtubule depolymerization / mitotic spindle elongation / negative regulation of microtubule depolymerization / protein hexamerization / positive regulation of dendrite morphogenesis / mitotic sister chromatid segregation / alpha-tubulin binding / isomerase activity / lipid droplet / adult locomotory behavior / locomotory behavior / neuromuscular junction / terminal bouton / microtubule cytoskeleton organization / spindle / microtubule cytoskeleton / chromosome / nervous system development / microtubule binding / microtubule / cell division / centrosome / ATP hydrolysis activity / ATP binding / membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Drosophila melanogaster (fruit fly) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9413185678 Å | |||||||||
Authors | Pisa, R. / Cupido, T. / Kapoor, T.M. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Cell Chem Biol / Year: 2019 Title: Analyzing Resistance to Design Selective Chemical Inhibitors for AAA Proteins. Authors: Pisa, R. / Cupido, T. / Steinman, J.B. / Jones, N.H. / Kapoor, T.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6p12.cif.gz | 92 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6p12.ent.gz | 53.5 KB | Display | PDB format |
PDBx/mmJSON format | 6p12.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p1/6p12 ftp://data.pdbj.org/pub/pdb/validation_reports/p1/6p12 | HTTPS FTP |
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-Related structure data
Related structure data | 6p10C 6p11C 6p13C 6p14C 3b9pS 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
#1: Protein | Mass: 34191.848 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: spas, CG5977 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8I0P1, microtubule-severing ATPase |
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#2: Chemical | ChemComp-NKY / |
#3: Chemical | ChemComp-SO4 / |
#4: Chemical | ChemComp-MPD / ( |
#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: 2.65 Å3/Da / Density % sol: 57.88 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.1 M sodium acetate, pH 5.0-7.0, 2% PEG4000, 15% MPD PH range: 5.0-7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9197 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 14, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9197 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→50 Å / Num. obs: 26363 / % possible obs: 99 % / Redundancy: 6.5 % / Biso Wilson estimate: 43.2284817795 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.031 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 1.94→1.97 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 1323 / CC1/2: 0.932 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3B9P Resolution: 1.9413185678→40.336 Å / SU ML: 0.256993797688 / Cross valid method: FREE R-VALUE / σ(F): 1.38937703476 / Phase error: 25.154924059
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.7947301096 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9413185678→40.336 Å
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Refine LS restraints |
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LS refinement shell |
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