+Open data
-Basic information
Entry | Database: PDB / ID: 5oi7 | ||||||
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Title | Human CEP85 - coiled coil domain 4 | ||||||
Components | Centrosomal protein of 85 kDa | ||||||
Keywords | PROTEIN BINDING / Centrosomes / centriole / CEP85 / STIL | ||||||
Function / homology | Function and homology information regulation of mitotic centrosome separation / pericentriolar material / chromosome segregation / negative regulation of protein kinase activity / spindle pole / centrosome / nucleolus / Golgi apparatus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.67 Å | ||||||
Authors | van Breugel, M. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Nat Commun / Year: 2018 Title: Direct binding of CEP85 to STIL ensures robust PLK4 activation and efficient centriole assembly. Authors: Liu, Y. / Gupta, G.D. / Barnabas, D.D. / Agircan, F.G. / Mehmood, S. / Wu, D. / Coyaud, E. / Johnson, C.M. / McLaughlin, S.H. / Andreeva, A. / Freund, S.M.V. / Robinson, C.V. / Cheung, S.W.T. ...Authors: Liu, Y. / Gupta, G.D. / Barnabas, D.D. / Agircan, F.G. / Mehmood, S. / Wu, D. / Coyaud, E. / Johnson, C.M. / McLaughlin, S.H. / Andreeva, A. / Freund, S.M.V. / Robinson, C.V. / Cheung, S.W.T. / Raught, B. / Pelletier, L. / 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 | 5oi7.cif.gz | 54.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5oi7.ent.gz | 39.1 KB | Display | PDB format |
PDBx/mmJSON format | 5oi7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5oi7_validation.pdf.gz | 429.3 KB | Display | wwPDB validaton report |
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Full document | 5oi7_full_validation.pdf.gz | 429.8 KB | Display | |
Data in XML | 5oi7_validation.xml.gz | 11 KB | Display | |
Data in CIF | 5oi7_validation.cif.gz | 15.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oi/5oi7 ftp://data.pdbj.org/pub/pdb/validation_reports/oi/5oi7 | HTTPS FTP |
-Related structure data
Related structure data | 5oi9C 5oidC 2q6qS S: Starting model for refinement C: citing same article (ref.) |
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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: 10347.432 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CEP85, CCDC21 / Production host: Escherichia coli (E. coli) / Variant (production host): C41 / References: UniProt: Q6P2H3 #2: Chemical | ChemComp-MPD / ( | #3: 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: 2.17 Å3/Da / Density % sol: 43.29 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop Details: 100 mM Na-HEPES, pH 7.7 200 mM Na-Citrate 36 % (v/v) MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54179 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 22, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 1.67→36.98 Å / Num. obs: 21341 / % possible obs: 98.9 % / Redundancy: 11.1 % / Rmerge(I) obs: 0.202 / Rpim(I) all: 0.063 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 1.67→1.76 Å / Redundancy: 10.1 % / Rmerge(I) obs: 1.552 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2852 / CC1/2: 0.474 / Rpim(I) all: 0.506 / % possible all: 92.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2Q6Q Resolution: 1.67→36.976 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 0.04 / Phase error: 27.3
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.67→36.976 Å
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Refine LS restraints |
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LS refinement shell |
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