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Yorodumi- PDB-3zyn: Crystal structure of the N-terminal leucine rich repeats of Netri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zyn | ||||||
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Title | Crystal structure of the N-terminal leucine rich repeats of Netrin-G Ligand-3 | ||||||
Components | LEUCINE-RICH REPEAT-CONTAINING PROTEIN 4B | ||||||
Keywords | CELL ADHESION / SYNAPSE | ||||||
Function / homology | Function and homology information Receptor-type tyrosine-protein phosphatases / regulation of postsynaptic density assembly / synaptic membrane adhesion / cerebellar mossy fiber / positive regulation of synapse assembly / regulation of presynapse assembly / postsynaptic density membrane / presynaptic membrane / signaling receptor binding / glutamatergic synapse / plasma membrane Similarity search - Function | ||||||
Biological species | MUS MUSCULUS (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Seiradake, E. / Coles, C.H. / Perestenko, P.V. / Harlos, K. / McIlhinney, R.A.J. / Aricescu, A.R. / Jones, E.Y. | ||||||
Citation | Journal: Embo J. / Year: 2011 Title: Structural Basis for Cell Surface Patterning Through Netring-Ngl Interactions. Authors: Seiradake, E. / Coles, C.H. / Perestenko, P.V. / Harlos, K. / Mcilhinney, R.A.J. / Aricescu, A.R. / Jones, E.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zyn.cif.gz | 260 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zyn.ent.gz | 212 KB | Display | PDB format |
PDBx/mmJSON format | 3zyn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zy/3zyn ftp://data.pdbj.org/pub/pdb/validation_reports/zy/3zyn | HTTPS FTP |
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-Related structure data
Related structure data | 3zygC 3zyiC 3zyjC 3zyoC 2id5S C: citing same article (ref.) 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 57 - 365 / Label seq-ID: 4 - 312
NCS oper: (Code: given Matrix: (0.8343, -0.1376, -0.5338), Vector: |
-Components
#1: Protein | Mass: 36874.219 Da / Num. of mol.: 2 / Fragment: N-TERMINAL LEUCINE RICH REPEATS, RESIDUES 57-365 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Cell line (production host): HEK293S / Production host: HOMO SAPIENS (human) / References: UniProt: P0C192 #2: Sugar | |
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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: 2.7 Å3/Da / Density % sol: 55 % / Description: NONE |
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Crystal grow | pH: 7 / Details: 0.8 M SUCCINIC ACID PH 7.0. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9796 |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 21, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→53 Å / Num. obs: 13296 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 3.2→3.28 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.2 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2ID5 Resolution: 3.2→52.94 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.851 / SU B: 58.717 / SU ML: 0.447 / Cross valid method: THROUGHOUT / ESU R Free: 0.562 / 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: 36.2 Å2
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Refinement step | Cycle: LAST / Resolution: 3.2→52.94 Å
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Refine LS restraints |
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