+Open data
-Basic information
Entry | Database: PDB / ID: 5i99 | ||||||
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Title | Crystal structure of mouse CNTN3 Ig5-Fn2 domains | ||||||
Components | Contactin-3 | ||||||
Keywords | CELL ADHESION / Neural cell adhesion molecule / Immunoglobulin-like domains / Fibronectin type III domains | ||||||
Function / homology | Function and homology information Post-translational modification: synthesis of GPI-anchored proteins / side of membrane / neuron projection development / cell adhesion / plasma membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å | ||||||
Authors | Nikolaienko, R.M. / Bouyain, S. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2016 Title: Structural Basis for Interactions Between Contactin Family Members and Protein-tyrosine Phosphatase Receptor Type G in Neural Tissues. Authors: Nikolaienko, R.M. / Hammel, M. / Dubreuil, V. / Zalmai, R. / Hall, D.R. / Mehzabeen, N. / Karuppan, S.J. / Harroch, S. / Stella, S.L. / Bouyain, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5i99.cif.gz | 171 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5i99.ent.gz | 133.6 KB | Display | PDB format |
PDBx/mmJSON format | 5i99.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i9/5i99 ftp://data.pdbj.org/pub/pdb/validation_reports/i9/5i99 | HTTPS FTP |
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-Related structure data
Related structure data | 5e4iC 5e4qSC 5e4sC 5e52C 5e53C 5e55C 5e5rC 5e5uC 5e7lC 1ev2S 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: 43128.445 Da / Num. of mol.: 1 / Fragment: Ig domains 1-4, UNP residues 406-801 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cntn3, Pang, Pcs / Plasmid: pET32HP / Production host: Escherichia coli (E. coli) / Strain (production host): Origami 2 (DE3) / References: UniProt: Q07409 |
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#2: Chemical | ChemComp-GOL / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.01 Å3/Da / Density % sol: 59.1 % / Mosaicity: 0.565 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 7.5% (w/v) PEG 8000, 50 mM Imidazole-HCl pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 8, 2014 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: ROSENBAUM-ROCK DOUBLE-CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.4→50 Å / Num. obs: 20578 / % possible obs: 98.2 % / Redundancy: 11.9 % / Biso Wilson estimate: 29.44 Å2 / Rmerge(I) obs: 0.165 / Χ2: 0.98 / Net I/av σ(I): 14.875 / Net I/σ(I): 5.9 / Num. measured all: 244693 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1EV2, 5E4Q Resolution: 2.4→43.095 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.84
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 101.26 Å2 / Biso mean: 41.1634 Å2 / Biso min: 17.01 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.4→43.095 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7
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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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