+Open data
-Basic information
Entry | Database: PDB / ID: 4icw | ||||||
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Title | N-terminal C2 domain of human CEP120 | ||||||
Components | Centrosomal protein of 120 kDaCentrosome | ||||||
Keywords | TRANSPORT PROTEIN / C2 domain / lipid binding | ||||||
Function / homology | Function and homology information positive regulation of centriole elongation / positive regulation of establishment of protein localization / positive regulation of centrosome duplication / interkinetic nuclear migration / astral microtubule organization / positive regulation of cilium assembly / centrosome cycle / centriole / neurogenesis / cerebral cortex development ...positive regulation of centriole elongation / positive regulation of establishment of protein localization / positive regulation of centrosome duplication / interkinetic nuclear migration / astral microtubule organization / positive regulation of cilium assembly / centrosome cycle / centriole / neurogenesis / cerebral cortex development / centrosome / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Janowski, R. / Guarin, N. / Coll, M. | ||||||
Citation | Journal: To be Published Title: N-terminal C2 domain tandem of human CEP120 shows lipid binding properties Authors: Janowski, R. / Guarin, N. / Speroni, S. / Serrano, L. / Coll, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4icw.cif.gz | 70.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4icw.ent.gz | 53.6 KB | Display | PDB format |
PDBx/mmJSON format | 4icw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ic/4icw ftp://data.pdbj.org/pub/pdb/validation_reports/ic/4icw | HTTPS FTP |
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-Related 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: 19407.268 Da / Num. of mol.: 1 / Fragment: C2 domain, UNP residues 1-151 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CEP120, CCDC100 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q8N960 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 9.5 Details: 25% (v/w) PEG 3000 , pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9726 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 20, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9726 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. all: 6902 / Num. obs: 6902 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 58.8 Å2 / Rmerge(I) obs: 0.029 / Net I/σ(I): 25.8 |
Reflection shell | Resolution: 2.2→2.26 Å / Rmerge(I) obs: 0.522 / Mean I/σ(I) obs: 3.06 / % possible all: 98.6 |
-Processing
Software | Name: REFMAC / Version: 5.5.0102 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.953 / SU B: 18.797 / SU ML: 0.206 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.365 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 84.758 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.318 Å / Total num. of bins used: 10
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Refinement TLS params. | Method: refined / Origin x: 11.3244 Å / Origin y: -8.0511 Å / Origin z: -13.9524 Å
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