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Yorodumi- PDB-4pfo: Myosin VI motor domain in the Pi release state, space group P212121 -
+Open data
-Basic information
Entry | Database: PDB / ID: 4pfo | ||||||||||||
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Title | Myosin VI motor domain in the Pi release state, space group P212121 | ||||||||||||
Components | Unconventional myosin-VI | ||||||||||||
Keywords | MOTOR PROTEIN / Myosin / motor domain / Pi Release state | ||||||||||||
Function / homology | Function and homology information myosin complex / clathrin-coated vesicle / microvillus / cytoskeletal motor activity / clathrin-coated pit / filopodium / sensory perception of sound / ruffle membrane / actin filament binding / Golgi apparatus / ATP binding Similarity search - Function | ||||||||||||
Biological species | Sus scrofa (pig) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||||||||
Authors | Isabet, T. / Benisty, H. / Llinas, P. / Sweeney, H.L. / Houdusse, A. | ||||||||||||
Funding support | France, United States, 3items
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Citation | Journal: Dev.Cell / Year: 2015 Title: How actin initiates the motor activity of Myosin. Authors: Llinas, P. / Isabet, T. / Song, L. / Ropars, V. / Zong, B. / Benisty, H. / Sirigu, S. / Morris, C. / Kikuti, C. / Safer, D. / Sweeney, H.L. / Houdusse, A. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4pfo.cif.gz | 326.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pfo.ent.gz | 258.5 KB | Display | PDB format |
PDBx/mmJSON format | 4pfo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pf/4pfo ftp://data.pdbj.org/pub/pdb/validation_reports/pf/4pfo | HTTPS FTP |
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-Related structure data
Related structure data | 4pfpC 4pjjC 4pjkC 4pjlC 4pjmC 4pjnC 4pk4C 2v26S 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: 89847.180 Da / Num. of mol.: 1 / Fragment: residues 2-789 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / Gene: MYO6 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: F1RQI7 | ||
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#2: Chemical | ChemComp-MG / | ||
#3: Chemical | ChemComp-ADP / | ||
#4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.37 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 6,25% PEG 8K, 50mM Tris pH 8,5, 1mM TCEP and 3% Glycerol with microseeding |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 11, 2010 |
Radiation | Monochromator: Si III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→45 Å / Num. obs: 90603 / % possible obs: 99.4 % / Redundancy: 8.5 % / Biso Wilson estimate: 35.2 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 16.38 |
Reflection shell | Resolution: 1.75→1.8 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 2.42 / % possible all: 94.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2v26 Resolution: 1.75→17.64 Å / Cor.coef. Fo:Fc: 0.9657 / Cor.coef. Fo:Fc free: 0.9621 / SU R Cruickshank DPI: 0.096 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.1 / SU Rfree Blow DPI: 0.094 / SU Rfree Cruickshank DPI: 0.092
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Displacement parameters | Biso mean: 39.39 Å2
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Refine analyze | Luzzati coordinate error obs: 0.223 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.75→17.64 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.79 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -1.1582 Å / Origin y: -3.8551 Å / Origin z: 13.6567 Å
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Refinement TLS group | Selection details: { A|* } |