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Yorodumi- PDB-6mga: Crystal Structure of Human Protocadherin-1 EC1-4 with glycosylation -
+Open data
-Basic information
Entry | Database: PDB / ID: 6mga | ||||||
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Title | Crystal Structure of Human Protocadherin-1 EC1-4 with glycosylation | ||||||
Components | Protocadherin-1 | ||||||
Keywords | CELL ADHESION / cadherins / adhesion / calcium-binding protein / asthma | ||||||
Function / homology | Function and homology information homophilic cell adhesion via plasma membrane adhesion molecules / cell-cell junction / cell-cell signaling / cell junction / nervous system development / cell adhesion / intracellular membrane-bounded organelle / calcium ion binding / nucleolus / nucleoplasm / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å | ||||||
Authors | Modak, D. / Sotomayor, M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Commun Biol / Year: 2019 Title: Identification of an adhesive interface for the non-clustered delta 1 protocadherin-1 involved in respiratory diseases. Authors: Modak, D. / Sotomayor, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6mga.cif.gz | 187.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6mga.ent.gz | 149.3 KB | Display | PDB format |
PDBx/mmJSON format | 6mga.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mg/6mga ftp://data.pdbj.org/pub/pdb/validation_reports/mg/6mga | HTTPS FTP |
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-Related structure data
Related structure data | 6bx7SC 6pimC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 50052.109 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PCDH1 / Cell line (production host): Expi 293F / Production host: Homo sapiens (human) / References: UniProt: Q08174 |
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#2: Sugar | ChemComp-NAG / |
#3: Sugar | ChemComp-MAN / |
#4: Chemical | ChemComp-CA / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.7 Å3/Da / Density % sol: 73.81 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1 M Magnesium Chloride, 0.05 M Tris HCl pH 8.5, 30% PEG 550 MME |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 15, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 3.15→50 Å / Num. obs: 17231 / % possible obs: 100 % / Redundancy: 36.4 % / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.013 / Rrim(I) all: 0.079 / Net I/σ(I): 58 |
Reflection shell | Resolution: 3.15→3.2 Å / Redundancy: 28.2 % / Rmerge(I) obs: 1.762 / Mean I/σ(I) obs: 2.5 / Num. unique all: 823 / Rpim(I) all: 0.321 / Rrim(I) all: 1.792 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6BX7 Resolution: 3.15→48.53 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.942 / SU B: 38.954 / SU ML: 0.299 / Cross valid method: THROUGHOUT / ESU R: 0.722 / ESU R Free: 0.381 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 146.584 Å2
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Refinement step | Cycle: 1 / Resolution: 3.15→48.53 Å
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Refine LS restraints |
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