+Open data
-Basic information
Entry | Database: PDB / ID: 8cl9 | ||||||||||||
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Title | Tubulin-DARPin D1 complex | ||||||||||||
Components |
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Keywords | CELL CYCLE / Drug-tubulin-complex Cell cycle inhibition | ||||||||||||
Function / homology | Function and homology information positive regulation of axon guidance / microtubule-based process / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / microtubule cytoskeleton organization / microtubule cytoskeleton / mitotic cell cycle / nervous system development / microtubule / protein heterodimerization activity ...positive regulation of axon guidance / microtubule-based process / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / microtubule cytoskeleton organization / microtubule cytoskeleton / mitotic cell cycle / nervous system development / microtubule / protein heterodimerization activity / GTPase activity / GTP binding / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | synthetic construct (others) Bos taurus (cattle) | ||||||||||||
Method | X-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||||||||
Authors | Wranik, M. / Bertrand, Q. / Weinert, T. / Kepa, M.W. / Steinmetz, M. / Standfuss, J. | ||||||||||||
Funding support | Switzerland, 3items
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Citation | Journal: Nat Commun / Year: 2023 Title: A multi-reservoir extruder for time-resolved serial protein crystallography and compound screening at X-ray free-electron lasers. Authors: Wranik, M. / Kepa, M.W. / Beale, E.V. / James, D. / Bertrand, Q. / Weinert, T. / Furrer, A. / Glover, H. / Gashi, D. / Carrillo, M. / Kondo, Y. / Stipp, R.T. / Khusainov, G. / Nass, K. / ...Authors: Wranik, M. / Kepa, M.W. / Beale, E.V. / James, D. / Bertrand, Q. / Weinert, T. / Furrer, A. / Glover, H. / Gashi, D. / Carrillo, M. / Kondo, Y. / Stipp, R.T. / Khusainov, G. / Nass, K. / Ozerov, D. / Cirelli, C. / Johnson, P.J.M. / Dworkowski, F. / Beale, J.H. / Stubbs, S. / Zamofing, T. / Schneider, M. / Krauskopf, K. / Gao, L. / Thorn-Seshold, O. / Bostedt, C. / Bacellar, C. / Steinmetz, M.O. / Milne, C. / Standfuss, J. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8cl9.cif.gz | 216.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8cl9.ent.gz | 167.8 KB | Display | PDB format |
PDBx/mmJSON format | 8cl9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cl/8cl9 ftp://data.pdbj.org/pub/pdb/validation_reports/cl/8cl9 | HTTPS FTP |
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-Related structure data
Related structure data | 8cl5C 8cl6C 8cl7C 8cl8C 8clbC 8clcC 8cldC 8cleC 8clfC 8clgC 8clhC C: citing same article (ref.) |
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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
-Protein , 3 types, 3 molecules ABF
#1: Protein | Mass: 48665.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P81947 |
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#2: Protein | Mass: 48391.410 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q6B856 |
#3: Protein | Mass: 16435.645 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) |
-Non-polymers , 3 types, 148 molecules
#4: Chemical | #5: Chemical | ChemComp-MG / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 2.44 Å3/Da / Density % sol: 49.54 % |
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Crystal grow | Temperature: 293 K / Method: batch mode / pH: 5.5 Details: 21% PEG3000 (w/v), 0.2 M Ammonium Sulfate, 0.1 M Bis-Tris Methane |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: Y |
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Diffraction source | Source: FREE ELECTRON LASER / Site: SwissFEL ARAMIS / Beamline: ESA / Wavelength: 1.03 Å |
Detector | Type: PSI JUNGFRAU 16M / Detector: PIXEL / Date: Feb 28, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→14.94 Å / Num. obs: 63162 / % possible obs: 100 % / Redundancy: 71.9 % / CC1/2: 0.931 / Net I/σ(I): 3.58 |
Reflection shell | Resolution: 2.1→2.2 Å / Mean I/σ(I) obs: 0.52 / Num. unique obs: 6206 / CC1/2: 0.323 |
Serial crystallography sample delivery | Method: injection |
Serial crystallography sample delivery injection | Carrier solvent: Hydroxyethylcellulose / Description: High-viscosity injection / Injector diameter: 75 µm |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→13 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.79 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→13 Å
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Refine LS restraints |
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LS refinement shell |
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