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Yorodumi- PDB-6due: Toxoplasma gondii MyoA, a Class-XIV myosin, in the pre-powerstrok... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6due | ||||||
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Title | Toxoplasma gondii MyoA, a Class-XIV myosin, in the pre-powerstroke state | ||||||
Components | Myosin A | ||||||
Keywords | MOTOR PROTEIN / Apicomplexan / Myosin / ATPase | ||||||
Function / homology | Function and homology information myosin complex / cytoskeletal motor activity / actin binding / ATP binding Similarity search - Function | ||||||
Biological species | Toxoplasma gondii (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å | ||||||
Authors | Powell, C.J. / Boulanger, M.J. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018 Title: Structural and mechanistic insights into the function of the unconventional class XIV myosin MyoA fromToxoplasma gondii. Authors: Powell, C.J. / Ramaswamy, R. / Kelsen, A. / Hamelin, D.J. / Warshaw, D.M. / Bosch, J. / Burke, J.E. / Ward, G.E. / Boulanger, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6due.cif.gz | 311.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6due.ent.gz | 249 KB | Display | PDB format |
PDBx/mmJSON format | 6due.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6due_validation.pdf.gz | 788 KB | Display | wwPDB validaton report |
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Full document | 6due_full_validation.pdf.gz | 794.3 KB | Display | |
Data in XML | 6due_validation.xml.gz | 27 KB | Display | |
Data in CIF | 6due_validation.cif.gz | 36.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/du/6due ftp://data.pdbj.org/pub/pdb/validation_reports/du/6due | HTTPS FTP |
-Related structure data
Related structure data | 4byfS S: Starting model for refinement |
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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 , 1 types, 1 molecules A
#1: Protein | Mass: 88298.398 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Toxoplasma gondii (strain ATCC 50853 / GT1) (eukaryote) Strain: ATCC 50853 / GT1 / Gene: TGGT1_235470 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: S7W634 |
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-Non-polymers , 5 types, 31 molecules
#2: Chemical | ChemComp-ADP / | ||
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#3: Chemical | ChemComp-ALF / | ||
#4: Chemical | ChemComp-MG / | ||
#5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47.08 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 1:1 protein solution to reservoir solution (22% PEG8000, 200 mM ammonium sulfate, 100 mM MES, pH 6.5), cryoprotectant: reservoir solution + 15% glycerol PH range: 6.5-7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.987 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 20, 2017 Details: Flat bent collimating Rh coated mirror, toroidal focussing mirror |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→85.95 Å / Num. obs: 24306 / % possible obs: 97.6 % / Redundancy: 3.8 % / Biso Wilson estimate: 49.28 Å2 / Rmerge(I) obs: 0.124 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.856 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3495 / % possible all: 96.7 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4BYF Resolution: 2.6→48.717 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.09 / Phase error: 31.13
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 180.27 Å2 / Biso mean: 68.7476 Å2 / Biso min: 28.04 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.6→48.717 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9
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Refinement TLS params. | Method: refined / Origin x: 20.9759 Å / Origin y: 2.0842 Å / Origin z: 21.2636 Å
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Refinement TLS group |
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