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- PDB-5ejy: Structure of Dictyostelium Discoideum Myosin VII MyTH4-FERM MF1 domain -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ejy | ||||||
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Title | Structure of Dictyostelium Discoideum Myosin VII MyTH4-FERM MF1 domain | ||||||
![]() | Myosin-I heavy chain | ||||||
![]() | MOTOR PROTEIN / Molecular motor / myosin / myosin tail / MyTH4-FERM | ||||||
Function / homology | ![]() spore germination / actin filament-based movement / filopodium tip / filopodium assembly / myosin complex / microfilament motor activity / cell-substrate adhesion / cell leading edge / cytoskeletal motor activity / phagocytic cup ...spore germination / actin filament-based movement / filopodium tip / filopodium assembly / myosin complex / microfilament motor activity / cell-substrate adhesion / cell leading edge / cytoskeletal motor activity / phagocytic cup / phagocytosis / filopodium / actin filament organization / cell morphogenesis / endocytosis / : / actin filament binding / actin cytoskeleton / actin binding / cell cortex / microtubule binding / ATP binding / membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sirigu, S. / Titus, M.A. / Houdusse, A. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 131.2 KB | Display | ![]() |
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PDB format | ![]() | 95 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1021.6 KB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 25.3 KB | Display | |
Data in CIF | ![]() | 37.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ejqC ![]() 5ejrC ![]() 5ejsC ![]() 3pvlS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 57437.789 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
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#2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.53 Å3/Da / Density % sol: 65.14 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 18% PEG 8000, 100 mM MES pH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 16, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97242 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 69695 / % possible obs: 99.3 % / Redundancy: 5.9 % / Rsym value: 0.057 / Net I/σ(I): 18.36 |
Reflection shell | Resolution: 1.9→1.96 Å / Redundancy: 5.14 % / Mean I/σ(I) obs: 2.27 / % possible all: 97.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3pvl Resolution: 1.9→43.308 Å / FOM work R set: 0.8307 / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 23.67 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.354 Å2 / ksol: 0.357 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 81.32 Å2 / Biso mean: 36.31 Å2 / Biso min: 16.22 Å2
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Refinement step | Cycle: final / Resolution: 1.9→43.308 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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