+Open data
-Basic information
Entry | Database: PDB / ID: 4ofd | |||||||||
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Title | Crystal Structure of mouse Neph1 D1-D2 | |||||||||
Components | Kin of IRRE-like protein 1 | |||||||||
Keywords | CELL ADHESION / Immunoglobulin superfamily / Kidney / Blood filtration / Protein Binding / N-linked Glycosylation / SIGNALING PROTEIN / Membrane / Extracellular | |||||||||
Function / homology | Function and homology information Nephrin family interactions / excretion / cell projection membrane / myosin binding / positive regulation of actin filament polymerization / negative regulation of protein phosphorylation / dendritic shaft / cell-cell adhesion / cell-cell junction / membrane => GO:0016020 ...Nephrin family interactions / excretion / cell projection membrane / myosin binding / positive regulation of actin filament polymerization / negative regulation of protein phosphorylation / dendritic shaft / cell-cell adhesion / cell-cell junction / membrane => GO:0016020 / membrane raft / perinuclear region of cytoplasm / plasma membrane Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.94 Å | |||||||||
Authors | Ozkan, E. / Garcia, K.C. | |||||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2014 Title: Extracellular Architecture of the SYG-1/SYG-2 Adhesion Complex Instructs Synaptogenesis. Authors: Ozkan, E. / Chia, P.H. / Wang, R.R. / Goriatcheva, N. / Borek, D. / Otwinowski, Z. / Walz, T. / Shen, K. / Garcia, K.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ofd.cif.gz | 89.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ofd.ent.gz | 67 KB | Display | PDB format |
PDBx/mmJSON format | 4ofd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/of/4ofd ftp://data.pdbj.org/pub/pdb/validation_reports/of/4ofd | HTTPS FTP |
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-Related structure data
Related structure data | 4of0SC 4of3C 4of6C 4of7C 4of8SC 4ofiC 4ofkC 4ofpC 4ofyC 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: 23440.311 Da / Num. of mol.: 2 / Fragment: D1-D2, UNP residues 48-253 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kirrel, Kirrel1, Neph1, Neph1 (Kirrel) / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): High Five / References: UniProt: Q80W68 #2: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source |
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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: 4.56 Å3/Da / Density % sol: 73.05 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 15% PEG 3,350, 3% Dextran sulfate, 0.1 M Sodium citrate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 295.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 31, 2009 |
Radiation | Monochromator: Double crystal Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.94→50 Å / Num. all: 7877 / Num. obs: 7856 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 156.42 Å2 / Rsym value: 0.092 / Net I/σ(I): 18.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entries 4OF0, 4OF8 Resolution: 3.94→48.895 Å / SU ML: 0.56 / σ(F): 0 / Phase error: 44.54 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.94→48.895 Å
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Refine LS restraints |
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LS refinement shell |
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