+Open data
-Basic information
Entry | Database: PDB / ID: 3mtr | ||||||
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Title | Crystal structure of the Ig5-FN1 tandem of human NCAM | ||||||
Components | Neural cell adhesion molecule 1Neural cell adhesion molecule | ||||||
Keywords | CELL ADHESION / NCAM / immunoglobulin domain / fibronectin type III repeat | ||||||
Function / homology | Function and homology information regulation of semaphorin-plexin signaling pathway / commissural neuron axon guidance / NCAM1 interactions / ECM proteoglycans / epithelial to mesenchymal transition / NCAM signaling for neurite out-growth / Signal transduction by L1 / Interferon gamma signaling / virus receptor activity / RAF/MAP kinase cascade ...regulation of semaphorin-plexin signaling pathway / commissural neuron axon guidance / NCAM1 interactions / ECM proteoglycans / epithelial to mesenchymal transition / NCAM signaling for neurite out-growth / Signal transduction by L1 / Interferon gamma signaling / virus receptor activity / RAF/MAP kinase cascade / collagen-containing extracellular matrix / cell adhesion / external side of plasma membrane / Golgi membrane / cell surface / extracellular region / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Molecular replacement, ARP / Resolution: 1.8 Å | ||||||
Authors | Lavie, A. / Foley, D.A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Structure and mutagenesis of neural cell adhesion molecule domains: evidence for flexibility in the placement of polysialic acid attachment sites Authors: Foley, D.A. / Swartzentruber, K.G. / Lavie, A. / Colley, K.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mtr.cif.gz | 96.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mtr.ent.gz | 72.5 KB | Display | PDB format |
PDBx/mmJSON format | 3mtr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mt/3mtr ftp://data.pdbj.org/pub/pdb/validation_reports/mt/3mtr | HTTPS FTP |
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-Related structure data
Related structure data | 2hazS S: Starting model for refinement |
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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: 23417.867 Da / Num. of mol.: 2 / Fragment: Ig5-FN1 tandem (UNP residues 414 to 611) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NCAM1, NCAM / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / References: UniProt: P13591 #2: Chemical | ChemComp-SO4 / | #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: 2.3 Å3/Da / Density % sol: 46.53 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 25% PEG 3350, 0.2 M ammonium sulfate, 0.1 M bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 15, 2008 |
Radiation | Monochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→30 Å / Num. obs: 40353 / % possible obs: 98.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): -3 / Rsym value: 0.095 / Net I/σ(I): 14.92 |
Reflection shell | Resolution: 1.79→1.9 Å / Mean I/σ(I) obs: 6.11 / Num. unique all: 6259 / Rsym value: 0.585 / % possible all: 96.3 |
-Processing
Software |
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Refinement | Method to determine structure: Molecular replacement, ARP Starting model: PDB entry 2HAZ Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.922 / SU B: 5.384 / SU ML: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.133 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.848 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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