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Yorodumi- PDB-5hzi: Crystal structure of photoinhibitable Intersectin1 containing C45... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5hzi | ||||||
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Title | Crystal structure of photoinhibitable Intersectin1 containing C450M mutant LOV2 domain | ||||||
Components | Intersectin-1,NPH1-1,Intersectin-1 | ||||||
Keywords | SIGNALING PROTEIN / Photoswitch / Chimera | ||||||
Function / homology | Function and homology information clathrin-dependent synaptic vesicle endocytosis / intracellular vesicle / blue light photoreceptor activity / proline-rich region binding / regulation of small GTPase mediated signal transduction / endosomal transport / NRAGE signals death through JNK / exocytosis / RHOQ GTPase cycle / CDC42 GTPase cycle ...clathrin-dependent synaptic vesicle endocytosis / intracellular vesicle / blue light photoreceptor activity / proline-rich region binding / regulation of small GTPase mediated signal transduction / endosomal transport / NRAGE signals death through JNK / exocytosis / RHOQ GTPase cycle / CDC42 GTPase cycle / RHOG GTPase cycle / clathrin-coated pit / EPHB-mediated forward signaling / guanyl-nucleotide exchange factor activity / recycling endosome / nuclear envelope / Cargo recognition for clathrin-mediated endocytosis / G alpha (12/13) signalling events / protein localization / Clathrin-mediated endocytosis / protein transport / lamellipodium / presynaptic membrane / molecular adaptor activity / non-specific serine/threonine protein kinase / intracellular signal transduction / neuron projection / protein serine/threonine kinase activity / calcium ion binding / ATP binding / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Avena sativa (oats) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Tarnawski, M. / Dagliyan, O. / Chu, P.H. / Shirvanyants, D. / Dokholyan, N.V. / Hahn, K.M. / Schlichting, I. | ||||||
Citation | Journal: Science / Year: 2016 Title: Engineering extrinsic disorder to control protein activity in living cells. Authors: Dagliyan, O. / Tarnawski, M. / Chu, P.H. / Shirvanyants, D. / Schlichting, I. / Dokholyan, N.V. / Hahn, K.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5hzi.cif.gz | 405.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hzi.ent.gz | 332.9 KB | Display | PDB format |
PDBx/mmJSON format | 5hzi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5hzi_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 5hzi_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 5hzi_validation.xml.gz | 34.5 KB | Display | |
Data in CIF | 5hzi_validation.cif.gz | 45.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hz/5hzi ftp://data.pdbj.org/pub/pdb/validation_reports/hz/5hzi | HTTPS FTP |
-Related structure data
Related structure data | 5hzhC 5hzjC 5hzkC 1ki1S 2wkqS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 58309.168 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Avena sativa (oats) Gene: ITSN1, ITSN, SH3D1A, NPH1-1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15811, UniProt: O49003 #2: Chemical | #3: 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: 2.62 Å3/Da / Density % sol: 53.07 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 0.1 M HEPES pH 7.5, 9% (w/v) PEG 8000, 9% (v/v) ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99998 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 21, 2014 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99998 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 36823 / % possible obs: 99.4 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.9 |
Reflection shell | Resolution: 2.6→2.7 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.548 / Mean I/σ(I) obs: 3.6 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1KI1, 2WKQ Resolution: 2.6→47.153 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 34.43
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→47.153 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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