+Open data
-Basic information
Entry | Database: PDB / ID: 1cs6 | ||||||
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Title | N-TERMINAL FRAGMENT OF AXONIN-1 FROM CHICKEN | ||||||
Components | AXONIN-1 | ||||||
Keywords | CELL ADHESION / NEURAL CELL ADHESION | ||||||
Function / homology | Function and homology information presynaptic membrane organization / : / neuron cell-cell adhesion / cell adhesion molecule binding / plasma membrane Similarity search - Function | ||||||
Biological species | Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å | ||||||
Authors | Freigang, J. / Proba, K. / Diederichs, K. / Sonderegger, P. / Welte, W. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2000 Title: The crystal structure of the ligand binding module of axonin-1/TAG-1 suggests a zipper mechanism for neural cell adhesion. Authors: Freigang, J. / Proba, K. / Leder, L. / Diederichs, K. / Sonderegger, P. / Welte, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1cs6.cif.gz | 91 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cs6.ent.gz | 71.9 KB | Display | PDB format |
PDBx/mmJSON format | 1cs6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1cs6_validation.pdf.gz | 378.7 KB | Display | wwPDB validaton report |
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Full document | 1cs6_full_validation.pdf.gz | 381.4 KB | Display | |
Data in XML | 1cs6_validation.xml.gz | 9.4 KB | Display | |
Data in CIF | 1cs6_validation.cif.gz | 15.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cs/1cs6 ftp://data.pdbj.org/pub/pdb/validation_reports/cs/1cs6 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is an oligomer generated by the two-fold screw axis. |
-Components
#1: Protein | Mass: 42602.734 Da / Num. of mol.: 1 / Fragment: IG1-4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Plasmid: PTFT / Production host: Escherichia coli (E. coli) / References: UniProt: P28685 |
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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: 3.2 Å3/Da / Density % sol: 61.6 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: PEG 10000, sodium formiate, HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 17 ℃ / pH: 8.5 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: X11 / Wavelength: 0.91 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 20, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. all: 50527 / Num. obs: 48051 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Biso Wilson estimate: 14.4 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 2 % / Rmerge(I) obs: 0.206 / Num. unique all: 3896 / % possible all: 83.3 |
Reflection shell | *PLUS % possible obs: 83.3 % / Mean I/σ(I) obs: 3.6 |
-Processing
Software |
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Refinement | Resolution: 1.8→20 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 566597.63 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 48.17 Å2 / ksol: 0.357 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.4 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 33 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.284 / % reflection Rfree: 4.7 % / Rfactor Rwork: 0.265 |