+Open data
-Basic information
Entry | Database: PDB / ID: 2drk | ||||||
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Title | Acanthamoeba myosin I SH3 domain bound to Acan125 | ||||||
Components |
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Keywords | CONTRACTILE PROTEIN / SH3 domain | ||||||
Function / homology | Function and homology information plasma membrane bounded cell projection / cellular component assembly / vesicle transport along actin filament / myosin complex / microfilament motor activity / cell leading edge / actin filament organization / actin filament binding / endocytosis / vesicle ...plasma membrane bounded cell projection / cellular component assembly / vesicle transport along actin filament / myosin complex / microfilament motor activity / cell leading edge / actin filament organization / actin filament binding / endocytosis / vesicle / ATP binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Acanthamoeba castellanii (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å | ||||||
Authors | Houdusse, A. / Bahloul, A. / Ostap, E.M. | ||||||
Citation | Journal: To be Published Title: The crystal structure of the SH3 domain of Acanthamoeba myosin IB bound to Acan125 Authors: Houdusse, A. / Bahloul, A. / Ostap, E.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2drk.cif.gz | 28.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2drk.ent.gz | 17.6 KB | Display | PDB format |
PDBx/mmJSON format | 2drk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dr/2drk ftp://data.pdbj.org/pub/pdb/validation_reports/dr/2drk | HTTPS FTP |
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-Related structure data
Related structure data | 2drmC 1semS C: citing same article (ref.) 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 6584.188 Da / Num. of mol.: 1 / Fragment: SH3 domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acanthamoeba castellanii (eukaryote) / Plasmid: pGEX / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P19706 |
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#2: Protein/peptide | Mass: 1103.339 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in Acanthamoeba / References: UniProt: P90630 |
#3: Chemical | ChemComp-GOL / |
#4: Chemical | ChemComp-SO4 / |
#5: 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: 1.74 Å3/Da / Density % sol: 29.38 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 278K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.86 Å |
Detector | Detector: CCD / Date: Jun 30, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.86 Å / Relative weight: 1 |
Reflection | Resolution: 1.42→30 Å / Num. obs: 10624 |
Reflection shell | Resolution: 1.42→1.46 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1SEM Resolution: 1.42→28.4 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.054 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.067 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 9.161 Å2
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Refinement step | Cycle: LAST / Resolution: 1.42→28.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.42→1.457 Å / Total num. of bins used: 20
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