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Yorodumi- PDB-3zyo: Crystal structure of the N-terminal leucine rich repeats and immu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zyo | ||||||
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Title | Crystal structure of the N-terminal leucine rich repeats and immunoglobulin domain 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: 3.1 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 | 3zyo.cif.gz | 172.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zyo.ent.gz | 138.3 KB | Display | PDB format |
PDBx/mmJSON format | 3zyo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3zyo_validation.pdf.gz | 447.7 KB | Display | wwPDB validaton report |
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Full document | 3zyo_full_validation.pdf.gz | 451.4 KB | Display | |
Data in XML | 3zyo_validation.xml.gz | 15.8 KB | Display | |
Data in CIF | 3zyo_validation.cif.gz | 20.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zy/3zyo ftp://data.pdbj.org/pub/pdb/validation_reports/zy/3zyo | HTTPS FTP |
-Related structure data
Related structure data | 3zygC 3zyiC 3zyjC 3zynSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 46437.859 Da / Num. of mol.: 1 Fragment: N-TERMINAL LEUCINE RICH REPEATS AND IMMUNOGLOBULIN DOMAIN, RESIDUES 57-455 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 |
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#2: Chemical | ChemComp-ZN / |
#3: Sugar | ChemComp-NAG / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 0.1 M NAH2PO4, 0.1 M KH2PO4, 2M NACL, 0.1 M MES, PH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.0714 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Aug 5, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0714 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→38.6 Å / Num. obs: 10743 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 7.3 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 3.1→3.27 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 2.6 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3ZYN Resolution: 3.1→38.6 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.889 / SU B: 49.006 / SU ML: 0.399 / Cross valid method: THROUGHOUT / ESU R Free: 0.469 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. CLEAR ELECTRON DENSITY FOR AMINO ACID RESIDUES Q68-A69 AND N335-C338 WAS NOT OBSERVED AND THESE ARE OMITTED FROM THE MODEL. DISORDERED ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. CLEAR ELECTRON DENSITY FOR AMINO ACID RESIDUES Q68-A69 AND N335-C338 WAS NOT OBSERVED AND THESE ARE OMITTED FROM THE MODEL. DISORDERED SIDECHAINS WERE MODELED STEREOCHEMICALLY
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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: 87.797 Å2
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Refinement step | Cycle: LAST / Resolution: 3.1→38.6 Å
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