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Yorodumi- PDB-1pz7: Modulation of agrin function by alternative splicing and Ca2+ binding -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pz7 | ||||||
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Title | Modulation of agrin function by alternative splicing and Ca2+ binding | ||||||
Components | Agrin | ||||||
Keywords | STRUCTURAL PROTEIN / Agrin | ||||||
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 / extracellular matrix binding / heparan sulfate proteoglycan binding / positive regulation of filopodium assembly / neuromuscular junction development / transmembrane receptor protein tyrosine kinase activator activity / receptor clustering / basement membrane / laminin binding / extracellular matrix / brain development / neuromuscular junction / G protein-coupled acetylcholine receptor signaling pathway / positive regulation of GTPase activity / negative regulation of neuron projection development / signaling receptor activity / heparin binding / nervous system development / 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: 1.421 Å | ||||||
Authors | Stetefeld, J. / Alexandrescu, A.T. / Maciejewski, M.W. / Jenny, M. / Rathgeb-Szabo, K. / Schulthess, T. / Landwehr, R. / Frank, S. / Ruegg, M.A. / Kammerer, R.A. | ||||||
Citation | Journal: STRUCTURE / Year: 2004 Title: Modulation of agrin function by alternative splicing and Ca2+ binding. Authors: Stetefeld, J. / Alexandrescu, A.T. / Maciejewski, M.W. / Jenny, M. / Rathgeb-Szabo, K. / Schulthess, T. / Landwehr, R. / Frank, S. / Ruegg, M.A. / Kammerer, R.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pz7.cif.gz | 91.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pz7.ent.gz | 73.8 KB | Display | PDB format |
PDBx/mmJSON format | 1pz7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pz/1pz7 ftp://data.pdbj.org/pub/pdb/validation_reports/pz/1pz7 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 22345.291 Da / Num. of mol.: 2 / Fragment: BASAL LAMINA DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: AGRN / Production host: Escherichia coli (E. coli) / References: UniProt: P31696 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 5 |
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-Sample preparation
Crystal | Density Matthews: 1.94 Å3/Da / Density % sol: 36.61 % |
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Crystal grow | Temperature: 276 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: peg 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 276K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: X31 / Wavelength: 0.97834 Å |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97834 Å / Relative weight: 1 |
Reflection | Resolution: 1.42→24.4 Å / Num. obs: 63594 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rsym value: 0.043 / Net I/σ(I): 8.2 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.421→20 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.01 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.082 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.698 Å2
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Refinement step | Cycle: LAST / Resolution: 1.421→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.421→1.458 Å / Total num. of bins used: 20 /
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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