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Yorodumi- PDB-6hxy: Crystal structure of the head and coiled-coil domains of zebrafis... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6hxy | ||||||
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Title | Crystal structure of the head and coiled-coil domains of zebrafish CCDC61 | ||||||
Components | Coiled-coil domain-containing protein 61 | ||||||
Keywords | STRUCTURAL PROTEIN / Centrosome / cilia / scaffold protein / proto-filament | ||||||
Function / homology | Function and homology information centriolar subdistal appendage / centriole assembly / cell projection organization / microtubule organizing center / centriolar satellite / mitotic spindle assembly / ciliary basal body / centrosome / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Danio rerio (zebrafish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Ochi, T. / van Breugel, M. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Structure / Year: 2020 Title: CCDC61/VFL3 Is a Paralog of SAS6 and Promotes Ciliary Functions. Authors: Ochi, T. / Quarantotti, V. / Lin, H. / Jullien, J. / Rosa E Silva, I. / Boselli, F. / Barnabas, D.D. / Johnson, C.M. / McLaughlin, S.H. / Freund, S.M.V. / Blackford, A.N. / Kimata, Y. / ...Authors: Ochi, T. / Quarantotti, V. / Lin, H. / Jullien, J. / Rosa E Silva, I. / Boselli, F. / Barnabas, D.D. / Johnson, C.M. / McLaughlin, S.H. / Freund, S.M.V. / Blackford, A.N. / Kimata, Y. / Goldstein, R.E. / Jackson, S.P. / Blundell, T.L. / Dutcher, S.K. / Gergely, F. / van Breugel, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hxy.cif.gz | 133 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hxy.ent.gz | 104.2 KB | Display | PDB format |
PDBx/mmJSON format | 6hxy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hx/6hxy ftp://data.pdbj.org/pub/pdb/validation_reports/hx/6hxy | HTTPS FTP |
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-Related structure data
Related structure data | 6hxtC 6hxvSC 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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Unit cell |
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-Components
#1: Protein | Mass: 19537.479 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Danio rerio (zebrafish) / Gene: ccdc61, zgc:153153 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q08CF3 #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: 4.07 Å3/Da / Density % sol: 69.74 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 1 M LiCl, 100 mM Citric acid |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 8, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→68.31 Å / Num. obs: 14498 / % possible obs: 100 % / Redundancy: 5.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.051 / Rrim(I) all: 0.124 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 2.9→3.08 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.849 / Mean I/σ(I) obs: 2 / Num. unique obs: 2302 / CC1/2: 0.84 / Rpim(I) all: 0.375 / Rrim(I) all: 0.93 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6HXV Resolution: 2.9→67.879 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.81
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 83.16 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→67.879 Å
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Refine LS restraints |
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LS refinement shell |
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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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