+Open data
-Basic information
Entry | Database: PDB / ID: 6hxt | |||||||||
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Title | Crystal structure of the head domain of human CCDC61 | |||||||||
Components | Coiled-coil domain-containing protein 61 | |||||||||
Keywords | STRUCTURAL PROTEIN / Centrosome / cilia / scaffold protein / protfilament | |||||||||
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 / microtubule binding / centrosome / identical protein binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.55 Å | |||||||||
Authors | Ochi, T. / Blundell, T.L. / van Breugel, M. | |||||||||
Funding support | United Kingdom, 2items
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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 | 6hxt.cif.gz | 156 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hxt.ent.gz | 129.1 KB | Display | PDB format |
PDBx/mmJSON format | 6hxt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hx/6hxt ftp://data.pdbj.org/pub/pdb/validation_reports/hx/6hxt | HTTPS FTP |
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-Related 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: 16737.164 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CCDC61 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9Y6R9 #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: 2.3 Å3/Da / Density % sol: 46.43 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.3 / Details: 8%(w/v) PEG6,000, 100 mM Tris-HC |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 7, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→29.68 Å / Num. obs: 15498 / % possible obs: 99.1 % / Redundancy: 5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.037 / Rrim(I) all: 0.086 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 2.55→2.66 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.568 / Num. unique obs: 1872 / CC1/2: 0.932 / Rpim(I) all: 0.266 / Rrim(I) all: 0.63 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.55→29.68 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 30.86
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 69.81 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.55→29.68 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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