[English] 日本語
Yorodumi- PDB-1jb3: The Laminin-Binding Domain of Agrin is structurally related to N-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jb3 | ||||||
---|---|---|---|---|---|---|---|
Title | The Laminin-Binding Domain of Agrin is structurally related to N-TIMP-1 | ||||||
Components | Agrin | ||||||
Keywords | CELL ADHESION / neuromuscular junction / agrin / interaction coiled-doil proteins with globular proteins / OB-fold / TIMP | ||||||
Function / homology | Function and homology information extracellular matrix of synaptic cleft / acetylcholine receptor regulator activity / positive regulation of synaptic assembly at neuromuscular junction / skeletal muscle acetylcholine-gated channel clustering / chondroitin sulfate binding / laminin-1 binding / sialic acid binding / neuron cell-cell adhesion / dystroglycan binding / basal part of cell ...extracellular matrix of synaptic cleft / acetylcholine receptor regulator activity / positive regulation of synaptic assembly at neuromuscular junction / skeletal muscle acetylcholine-gated channel clustering / chondroitin sulfate binding / laminin-1 binding / sialic acid binding / neuron cell-cell adhesion / dystroglycan binding / basal part of cell / photoreceptor ribbon synapse / filopodium assembly / glycosaminoglycan binding / heparan sulfate proteoglycan binding / extracellular matrix binding / positive regulation of filopodium assembly / neuromuscular junction development / transmembrane receptor protein tyrosine kinase activator activity / receptor clustering / basement membrane / laminin binding / extracellular matrix / positive regulation of GTPase activity / neuromuscular junction / G protein-coupled acetylcholine receptor signaling pathway / brain development / negative regulation of neuron projection development / nervous system development / signaling receptor activity / heparin binding / actin cytoskeleton organization / cell differentiation / membrane raft / axon / glutamatergic synapse / synapse / calcium ion binding / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å | ||||||
Authors | Stetefeld, J. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2001 Title: The laminin-binding domain of agrin is structurally related to N-TIMP-1. Authors: Stetefeld, J. / Jenny, M. / Schulthess, T. / Landwehr, R. / Schumacher, B. / Frank, S. / Ruegg, M.A. / Engel, J. / Kammerer, R.A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1jb3.cif.gz | 41.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1jb3.ent.gz | 28.5 KB | Display | PDB format |
PDBx/mmJSON format | 1jb3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jb3_validation.pdf.gz | 423.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1jb3_full_validation.pdf.gz | 427.5 KB | Display | |
Data in XML | 1jb3_validation.xml.gz | 9.7 KB | Display | |
Data in CIF | 1jb3_validation.cif.gz | 13.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jb/1jb3 ftp://data.pdbj.org/pub/pdb/validation_reports/jb/1jb3 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 15131.321 Da / Num. of mol.: 1 / Fragment: Laminin-Binding Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Production host: Escherichia coli (E. coli) / References: UniProt: Q90685, UniProt: P31696*PLUS |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.8125 Å3/Da / Density % sol: 56 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: PEG4000, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 5.2 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95, 0.97842, 0.97928, 1.2 | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
| |||||||||||||||
Reflection | Resolution: 1.6→30 Å / Num. obs: 22609 / % possible obs: 94.3 % / Observed criterion σ(I): 5 / Redundancy: 2.3 % / Biso Wilson estimate: 22.6 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.06 / Net I/σ(I): 5 | |||||||||||||||
Reflection shell | Resolution: 1.6→1.66 Å / Rmerge(I) obs: 0.283 / Mean I/σ(I) obs: 5 / Rsym value: 0.325 | |||||||||||||||
Reflection | *PLUS Rmerge(I) obs: 0.06 | |||||||||||||||
Reflection shell | *PLUS % possible obs: 93.6 % / Rmerge(I) obs: 0.325 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 1.6→8 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1712138.96 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 77 Å2 / ksol: 0.537 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.3 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.6→1.7 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 9.9 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 26.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.309 / % reflection Rfree: 9.9 % / Rfactor Rwork: 0.285 |