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- PDB-3p3y: Crystal structure of neurofascin homophilic adhesion complex in s... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3p3y | ||||||
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Title | Crystal structure of neurofascin homophilic adhesion complex in space group p6522 | ||||||
![]() | Neurofascin | ||||||
![]() | CELL ADHESION / Ig domains | ||||||
Function / homology | ![]() paranodal junction / Neurofascin interactions / cell-cell adhesion mediator activity / axon initial segment / peripheral nervous system development / node of Ranvier / Interaction between L1 and Ankyrins / ficolin-1-rich granule membrane / myelination / axon guidance ...paranodal junction / Neurofascin interactions / cell-cell adhesion mediator activity / axon initial segment / peripheral nervous system development / node of Ranvier / Interaction between L1 and Ankyrins / ficolin-1-rich granule membrane / myelination / axon guidance / brain development / cell-cell adhesion / axon / focal adhesion / Neutrophil degranulation / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Liu, H. / He, X. | ||||||
![]() | ![]() Title: Homophilic adhesion mechanism of neurofascin, a member of the l1 family of neural cell adhesion molecules. Authors: Liu, H. / Focia, P.J. / He, X. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 100.9 KB | Display | ![]() |
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PDB format | ![]() | 78.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 450.5 KB | Display | ![]() |
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Full document | ![]() | 464 KB | Display | |
Data in XML | ![]() | 24.4 KB | Display | |
Data in CIF | ![]() | 36.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 |
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Unit cell |
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Components
#1: Protein | Mass: 45285.199 Da / Num. of mol.: 1 / Fragment: N-terminal four Ig domains (UNP residues 25-428) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Sugar | ChemComp-NAG / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.11 Å3/Da / Density % sol: 70.08 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 1.4 ammonium sulfate, 0.1 M cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Aug 14, 2008 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54981 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. all: 23854 / Num. obs: 23568 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 42.6 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.054 / Net I/σ(I): 19.9 |
Reflection shell | Resolution: 2.6→2.7 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 2.4 / Num. unique all: 2390 / Rsym value: 0.427 / % possible all: 96.4 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 45.1788 Å2 / ksol: 0.24541 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 89 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→19.71 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | |||||||||||||||||||||||||
LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
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Xplor file |
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