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Yorodumi- PDB-5ejs: Structure of Dictyostelium Discoideum Myosin VII MyTH4-FERM MF2 d... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ejs | ||||||
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Title | Structure of Dictyostelium Discoideum Myosin VII MyTH4-FERM MF2 domain, mutant 1 | ||||||
Components | Myosin-I heavy chain | ||||||
Keywords | MOTOR PROTEIN / Myosin / motor myosin / myosin tail / MyTH4-FERM | ||||||
Function / homology | Function and homology information spore germination / actin filament-based movement / filopodium tip / filopodium assembly / vesicle transport along actin filament / myosin complex / microfilament motor activity / phagocytic cup / cell-substrate adhesion / cell leading edge ...spore germination / actin filament-based movement / filopodium tip / filopodium assembly / vesicle transport along actin filament / myosin complex / microfilament motor activity / phagocytic cup / cell-substrate adhesion / cell leading edge / cytoskeletal motor activity / phagocytosis / filopodium / actin filament organization / cell morphogenesis / : / actin filament binding / actin cytoskeleton / actin binding / cell cortex / microtubule binding / vesicle / ATP binding / membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Dictyostelium discoideum (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Planelles-Herrero, V.J. / Sirkia, H. / Sourigues, Y. / Titus, M.A. / Houdusse, A. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2016 Title: Myosin MyTH4-FERM structures highlight important principles of convergent evolution. Authors: Planelles-Herrero, V.J. / Blanc, F. / Sirigu, S. / Sirkia, H. / Clause, J. / Sourigues, Y. / Johnsrud, D.O. / Amigues, B. / Cecchini, M. / Gilbert, S.P. / Houdusse, A. / Titus, M.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ejs.cif.gz | 416.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ejs.ent.gz | 343.1 KB | Display | PDB format |
PDBx/mmJSON format | 5ejs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ej/5ejs ftp://data.pdbj.org/pub/pdb/validation_reports/ej/5ejs | HTTPS FTP |
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-Related structure data
Related structure data | 5ejqC 5ejrSC 5ejyC 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: 57204.969 Da / Num. of mol.: 2 / Mutation: K1181E, R1882E, K1909E, K1912E, K1913E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Gene: myoI, DDB_G0274455 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): AI / References: UniProt: Q9U1M8 #2: 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: 2.71 Å3/Da / Density % sol: 54.68 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 11.9% PEG 3350, 0.1M Bis-Tris Propane pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97918 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 11, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→46.51 Å / Num. obs: 35131 / % possible obs: 99.7 % / Redundancy: 12.9 % / Rsym value: 0.089 / Net I/σ(I): 26.42 |
Reflection shell | Resolution: 2.7→2.87 Å / Redundancy: 13.4 % / Mean I/σ(I) obs: 3.95 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5EJR Resolution: 2.7→38.91 Å / Cor.coef. Fo:Fc: 0.9273 / Cor.coef. Fo:Fc free: 0.9122 / SU R Cruickshank DPI: 1.113 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 2.595 / SU Rfree Blow DPI: 0.31 / SU Rfree Cruickshank DPI: 0.308
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Displacement parameters | Biso max: 232.39 Å2 / Biso mean: 79.33 Å2 / Biso min: 24.64 Å2
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Refine analyze | Luzzati coordinate error obs: 0.465 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.7→38.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.78 Å / Total num. of bins used: 18
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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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