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Yorodumi- PDB-7ac5: Structure of Tubulin Darpin complex 1 collected by rotation seria... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ac5 | ||||||
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Title | Structure of Tubulin Darpin complex 1 collected by rotation serial crystallography on a COC membrane at a synchrotron source | ||||||
Components |
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Keywords | CELL CYCLE | ||||||
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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å | ||||||
Authors | Martiel, I. / Olieric, N. / Wranik, M. / Padeste, C. / Karpik, A. / Huang, C.Y. / Wang, M. / Marsh, M. | ||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2021 Title: Versatile microporous polymer-based supports for serial macromolecular crystallography. Authors: Martiel, I. / Beale, J.H. / Karpik, A. / Huang, C.Y. / Vera, L. / Olieric, N. / Wranik, M. / Tsai, C.J. / Muhle, J. / Aurelius, O. / John, J. / Hogbom, M. / Wang, M. / Marsh, M. / Padeste, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ac5.cif.gz | 572.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ac5.ent.gz | 473.8 KB | Display | PDB format |
PDBx/mmJSON format | 7ac5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ac5_validation.pdf.gz | 402.4 KB | Display | wwPDB validaton report |
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Full document | 7ac5_full_validation.pdf.gz | 411.6 KB | Display | |
Data in XML | 7ac5_validation.xml.gz | 21.4 KB | Display | |
Data in CIF | 7ac5_validation.cif.gz | 33.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ac/7ac5 ftp://data.pdbj.org/pub/pdb/validation_reports/ac/7ac5 | HTTPS FTP |
-Related structure data
Related structure data | 7ac2C 7ac3C 7ac4C 7ac6C 7ai8C 7ai9C 5nquS 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
-Protein , 3 types, 3 molecules ABF
#1: Protein | Mass: 50204.445 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Production host: Escherichia coli (E. coli) / References: UniProt: P81947 |
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#2: Protein | Mass: 49999.887 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: TUBB2B / Production host: Escherichia coli (E. coli) / References: UniProt: Q6B856 |
#3: Protein | Mass: 18068.439 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Production host: Escherichia coli BL21(DE3) (bacteria) |
-Non-polymers , 5 types, 145 molecules
#4: Chemical | ChemComp-GTP / |
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#5: Chemical | ChemComp-MG / |
#6: Chemical | ChemComp-GDP / |
#7: Chemical | ChemComp-PG0 / |
#8: Water | ChemComp-HOH / |
-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: 2.37 Å3/Da / Density % sol: 48.02 % |
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Crystal grow | Temperature: 293 K / Method: batch mode Details: 26% PEG 3000, 0.2 M ammonium sulfate and 0.1 M bis-tris methane pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 9, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.26→49.212 Å / Num. obs: 49614 / % possible obs: 94.1 % / Redundancy: 8.22 % / CC1/2: 0.974 / Net I/σ(I): 4.48 |
Reflection shell | Resolution: 2.26→2.32 Å / Mean I/σ(I) obs: 0.64 / Num. unique obs: 4049 / CC1/2: 0.126 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5NQU Resolution: 2.26→49.212 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.72 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 162.8 Å2 / Biso mean: 62.0418 Å2 / Biso min: 24.42 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.26→49.212 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: 90.0986 Å / Origin y: 20.5259 Å / Origin z: 26.5948 Å
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Refinement TLS group |
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