[English] 日本語
Yorodumi- PDB-5ejq: Structure of Dictyostelium Discoideum Myosin VII MyTH4-FERM MF1 d... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ejq | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of Dictyostelium Discoideum Myosin VII MyTH4-FERM MF1 domain, mutant 2 | ||||||
Components | Myosin-I heavy chain | ||||||
Keywords | MOTOR PROTEIN / 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 / molecular replacement / Resolution: 2.19 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5ejq.cif.gz | 129.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5ejq.ent.gz | 96.4 KB | Display | PDB format |
PDBx/mmJSON format | 5ejq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ej/5ejq ftp://data.pdbj.org/pub/pdb/validation_reports/ej/5ejq | HTTPS FTP |
---|
-Related structure data
Related structure data | 5ejrC 5ejsC 5ejySC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 58772.055 Da / Num. of mol.: 1 / 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: Chemical | ChemComp-GLY / |
#3: Chemical | ChemComp-SER / |
#4: Chemical | ChemComp-GLU / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.14 % |
---|---|
Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 10% PEG 20K, 20% PEG 550 MME, 0.1M MOPS pH 7.5, 0.1M HEPES pH 7.5, 20 mM DL-Alanine, 20 mM DL-Glutamic acid, 20 mM Glycine, 20 mM DL-Lysine HCl, 20 mM DL-Serine |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97934 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: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 2.19→45.36 Å / Num. obs: 29999 / % possible obs: 99.97 % / Redundancy: 8.8 % / Rsym value: 0.057 / Net I/σ(I): 18.15 |
Reflection shell | Resolution: 2.19→2.32 Å / Redundancy: 8.9 % / Mean I/σ(I) obs: 6.14 / % possible all: 99.97 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR |
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5EJY Resolution: 2.19→19.01 Å / Cor.coef. Fo:Fc: 0.9535 / Cor.coef. Fo:Fc free: 0.9345 / SU R Cruickshank DPI: 0.256 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.299 / SU Rfree Blow DPI: 0.194 / SU Rfree Cruickshank DPI: 0.186
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 119.55 Å2 / Biso mean: 32.61 Å2 / Biso min: 12.29 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.233 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.19→19.01 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.19→2.27 Å / Total num. of bins used: 15
|