+Open data
-Basic information
Entry | Database: PDB / ID: 6l5j | ||||||
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Title | Crystal structure of human rootletin 1108-1317 | ||||||
Components | Rootletin | ||||||
Keywords | STRUCTURAL PROTEIN / centrosome / rootletin / coiled-coil | ||||||
Function / homology | Function and homology information subapical part of cell / establishment of organelle localization / ciliary basal body organization / centriole-centriole cohesion / 9+2 motile cilium / epithelial structure maintenance / protein localization to organelle / positive regulation of protein localization to cilium / positive regulation of cilium assembly / cellular homeostasis ...subapical part of cell / establishment of organelle localization / ciliary basal body organization / centriole-centriole cohesion / 9+2 motile cilium / epithelial structure maintenance / protein localization to organelle / positive regulation of protein localization to cilium / positive regulation of cilium assembly / cellular homeostasis / photoreceptor cell maintenance / centrosome cycle / ciliary rootlet / kinesin binding / photoreceptor inner segment / centriole / establishment of localization in cell / protein localization / structural constituent of cytoskeleton / actin cytoskeleton / actin binding / centrosome / structural molecule activity / extracellular exosome / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.77 Å | ||||||
Authors | Kim, J. / Choi, H.J. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: J.Mol.Biol. / Year: 2020 Title: Identification of a Structurally Dynamic Domain for Oligomer Formation in Rootletin. Authors: Ko, D. / Kim, J. / Rhee, K. / Choi, H.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6l5j.cif.gz | 263.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6l5j.ent.gz | 209 KB | Display | PDB format |
PDBx/mmJSON format | 6l5j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l5/6l5j ftp://data.pdbj.org/pub/pdb/validation_reports/l5/6l5j | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 25118.439 Da / Num. of mol.: 4 / Mutation: L1153M, L1166M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CROCC, KIAA0445 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5TZA2 Has ligand of interest | N | |
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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: 2.8 Å3/Da / Density % sol: 56.02 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M Tris pH 7.5, 4% PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97942 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 25, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97942 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.77→50 Å / Num. obs: 25990 / % possible obs: 95.1 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.064 / Rrim(I) all: 0.119 / Χ2: 1.246 / Net I/σ(I): 4.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.77→47.473 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 41.96
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 169.81 Å2 / Biso mean: 79.8283 Å2 / Biso min: 38.29 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.77→47.473 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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