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Yorodumi- PDB-6a9c: Crystal Structure c-terminal SH3 domain of Myosin IB from Entamoe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6a9c | ||||||
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Title | Crystal Structure c-terminal SH3 domain of Myosin IB from Entamoeba histolytica bound to EhFP10(GEF) peptide. | ||||||
Components |
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Keywords | CONTRACTILE PROTEIN / SH3 / MyosinI / Entamoeba histolytica / EhMySH3 | ||||||
Function / homology | Function and homology information phagosome reneutralization / lateral pseudopodium retraction / phagocytic cup lip / regulation of post-lysosomal vacuole size / actin wave / macropinocytic cup cytoskeleton / myosin I complex / chemotaxis to cAMP / pinocytosis / leading edge of lamellipodium ...phagosome reneutralization / lateral pseudopodium retraction / phagocytic cup lip / regulation of post-lysosomal vacuole size / actin wave / macropinocytic cup cytoskeleton / myosin I complex / chemotaxis to cAMP / pinocytosis / leading edge of lamellipodium / myosin light chain binding / actin-myosin filament sliding / actomyosin / filopodium assembly / endosomal transport / microfilament motor activity / exocytosis / phagocytosis / guanyl-nucleotide exchange factor activity / filopodium / actin filament organization / cell motility / phospholipid binding / actin filament binding / endocytosis / phagocytic vesicle membrane / cell-cell junction / actin cytoskeleton / early endosome / cytoskeleton / intracellular signal transduction / ATP binding / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Entamoeba histolytica (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å | ||||||
Authors | Gautam, G. / Gourinath, S. | ||||||
Citation | Journal: Plos Pathog. / Year: 2019 Title: EhFP10: A FYVE family GEF interacts with myosin IB to regulate cytoskeletal dynamics during endocytosis in Entamoeba histolytica. Authors: Gautam, G. / Ali, M.S. / Bhattacharya, A. / Gourinath, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6a9c.cif.gz | 42.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6a9c.ent.gz | 28.6 KB | Display | PDB format |
PDBx/mmJSON format | 6a9c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6a9c_validation.pdf.gz | 455.7 KB | Display | wwPDB validaton report |
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Full document | 6a9c_full_validation.pdf.gz | 455.3 KB | Display | |
Data in XML | 6a9c_validation.xml.gz | 7.7 KB | Display | |
Data in CIF | 6a9c_validation.cif.gz | 9.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a9/6a9c ftp://data.pdbj.org/pub/pdb/validation_reports/a9/6a9c | HTTPS FTP |
-Related structure data
Related structure data | 5xggS 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
#1: Protein | Mass: 7747.666 Da / Num. of mol.: 2 / Fragment: SH3 domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Gene: EHI_110810 / Production host: Escherichia coli (E. coli) / References: UniProt: C4LUC7 #2: Protein/peptide | | Mass: 1017.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Entamoeba histolytica (eukaryote) / References: UniProt: C4M4E9 #3: Chemical | #4: 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: 2.66 Å3/Da / Density % sol: 53.83 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.2M Ammonium sulphate, 30% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 19, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→50.78 Å / Num. obs: 12177 / % possible obs: 100 % / Redundancy: 14 % / CC1/2: 0.9 / Rmerge(I) obs: 0.103 / Rsym value: 0.103 / Net I/σ(I): 27.76 |
Reflection shell | Resolution: 1.98→2.01 Å / Mean I/σ(I) obs: 3.3 / Num. unique obs: 1153 / CC1/2: 0.98 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5xgg Resolution: 1.98→50.78 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.94 / SU B: 4.188 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.153 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.87 Å2
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Refinement step | Cycle: 1 / Resolution: 1.98→50.78 Å
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Refine LS restraints |
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