+Open data
-Basic information
Entry | Database: PDB / ID: 2xy1 | |||||||||
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Title | CRYSTAL STRUCTURE OF NCAM2 IG3-4 | |||||||||
Components | NEURAL CELL ADHESION MOLECULE 2 | |||||||||
Keywords | CELL ADHESION | |||||||||
Function / homology | Function and homology information neuron cell-cell adhesion / axonal fasciculation / nuclear body / axon / membrane / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | HOMO SAPIENS (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.979 Å | |||||||||
Authors | Kulahin, N. / Rasmussen, K.K. / Kristensen, O. / Berezin, V. / Bock, E. / Walmod, P.S. / Gajhede, M. | |||||||||
Citation | Journal: Structure / Year: 2011 Title: Structural Model and Trans-Interaction of the Entire Ectodomain of the Olfactory Cell Adhesion Molecule. Authors: Kulahin, N. / Kristensen, O. / Rasmussen, K.K. / Olsen, L. / Rydberg, P. / Vestergaard, B. / Kastrup, J.S. / Berezin, V. / Bock, E. / Walmod, P.S. / Gajhede, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xy1.cif.gz | 50.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xy1.ent.gz | 38.7 KB | Display | PDB format |
PDBx/mmJSON format | 2xy1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xy/2xy1 ftp://data.pdbj.org/pub/pdb/validation_reports/xy/2xy1 | 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: 21276.721 Da / Num. of mol.: 1 / Fragment: IG3-4, RESIDUES 209-398 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: PICHIA PASTORIS (fungus) / References: UniProt: O15394 | ||
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#2: Sugar | #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: 2.1 Å3/Da / Density % sol: 41.32 % / Description: NONE |
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Crystal grow | pH: 7 / Details: 25% PEG-6000, 0.1 M HEPES PH7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 16, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→20.17 Å / Num. obs: 12018 / % possible obs: 96.8 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 27.15 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 1.98→2.03 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.6 / % possible all: 90.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.979→19.993 Å / SU ML: 0.23 / σ(F): 1.35 / Phase error: 31.05 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.636 Å2 / ksol: 0.339 e/Å3 | |||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.979→19.993 Å
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Refine LS restraints |
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LS refinement shell |
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