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Yorodumi- PDB-3l7h: Insights into dynein assembly from a dynein intermediate chain li... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3l7h | ||||||
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Title | Insights into dynein assembly from a dynein intermediate chain light chain Roadblock structure | ||||||
Components | RE64145p | ||||||
Keywords | PROTEIN TRANSPORT / LC7 / Km23 / Roadblock / Dynein / Light Chain / Hydrolase | ||||||
Function / homology | Function and homology information axonemal dynein complex / mushroom body development / cytoplasmic dynein complex / dendrite morphogenesis / dynein intermediate chain binding / microtubule-based movement / microtubule / centrosome / cytoplasm Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Hall, J. / Karplus, P.A. / Barbar, E. | ||||||
Citation | Journal: To be Published Title: Insights into dynein assembly from a dynein intermediate chain light chain Roadblock structure Authors: Hall, J. / Karplus, P.A. / Barbar, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3l7h.cif.gz | 158.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3l7h.ent.gz | 127.5 KB | Display | PDB format |
PDBx/mmJSON format | 3l7h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l7/3l7h ftp://data.pdbj.org/pub/pdb/validation_reports/l7/3l7h | HTTPS FTP |
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-Related structure data
Related structure data | 2hz5S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 10837.399 Da / Num. of mol.: 4 / Fragment: LC7 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CG10751, Dmel_CG10751, robl / Plasmid: petDE3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q7KMS3 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.33 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 20% iso-propanol, 20% PEG 4000, 100 mM sodium citrate., pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K |
-Data collection
Diffraction | Mean temperature: 133.15 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 14, 2009 |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→63.72 Å / Num. all: 30082 / Num. obs: 27041 / % possible obs: 98.9 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.139 / Rsym value: 0.122 / Net I/σ(I): 2.5 |
Reflection shell | Resolution: 1.95→2.001 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.092 / Mean I/σ(I) obs: 5.5 / Rsym value: 0.4 / % possible all: 94.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 2HZ5 Resolution: 1.95→63.72 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.922 / SU B: 9.401 / SU ML: 0.121 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.181 / ESU R Free: 0.175 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.066 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→63.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.001 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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