+Open data
-Basic information
Entry | Database: PDB / ID: 3dvh | ||||||
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Title | LC8 Point mutant K36P | ||||||
Components | Dynein light chain 1, cytoplasmic | ||||||
Keywords | MOTOR PROTEIN / Dynein / DLC1 / light chain / PIN / LC8 / Cytoplasm / Microtubule | ||||||
Function / homology | Function and homology information spermatid nucleus elongation / chaeta morphogenesis / positive regulation of neuron remodeling / Macroautophagy / Aggrephagy / wing disc development / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / COPI-mediated anterograde transport / COPI-independent Golgi-to-ER retrograde traffic / chaeta development ...spermatid nucleus elongation / chaeta morphogenesis / positive regulation of neuron remodeling / Macroautophagy / Aggrephagy / wing disc development / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / COPI-mediated anterograde transport / COPI-independent Golgi-to-ER retrograde traffic / chaeta development / sperm individualization / microtubule anchoring at centrosome / imaginal disc-derived wing morphogenesis / Neutrophil degranulation / dynein complex / cytoplasmic dynein complex / dynein light intermediate chain binding / dynein intermediate chain binding / oogenesis / establishment of mitotic spindle orientation / actin filament bundle assembly / centriole / disordered domain specific binding / spermatogenesis / microtubule / protein homodimerization activity / protein-containing complex / cytoplasm Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Lightcap, C.M. / Williams, J.C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: Biochemical and structural characterization of the Pak1-LC8 interaction. Authors: Lightcap, C.M. / Sun, S. / Lear, J.D. / Rodeck, U. / Polenova, T. / Williams, J.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dvh.cif.gz | 64.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dvh.ent.gz | 48 KB | Display | PDB format |
PDBx/mmJSON format | 3dvh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dv/3dvh ftp://data.pdbj.org/pub/pdb/validation_reports/dv/3dvh | HTTPS FTP |
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-Related structure data
Related structure data | 3dvpC 3dvtC 2pg1S 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: 10603.067 Da / Num. of mol.: 3 / Mutation: K36P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: ctp, Cdlc1, ddlc1, CG6998 / Plasmid: pET21D / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q24117 #2: 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: 2.14 Å3/Da / Density % sol: 42.59 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 50 mM CaCl2, 100 mM HEPES, 28% (w/v) PEG MME 2000, 10% glycerol, 10 mM DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
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Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 1, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→28.9 Å / Num. obs: 18462 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Highest resolution: 2 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2PG1 monomer A Resolution: 2→27.2 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.925 / SU B: 4.341 / SU ML: 0.124 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.205 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.857 Å2
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Refinement step | Cycle: LAST / Resolution: 2→27.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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