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- PDB-5erp: Crystal structure of human Desmocollin-2 ectodomain fragment EC2-5 -
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Open data
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Basic information
Entry | Database: PDB / ID: 5erp | |||||||||
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Title | Crystal structure of human Desmocollin-2 ectodomain fragment EC2-5 | |||||||||
![]() | Desmocollin-2 | |||||||||
![]() | ![]() ![]() ![]() | |||||||||
Function / homology | ![]() cardiac muscle cell-cardiac muscle cell adhesion / bundle of His cell-Purkinje myocyte adhesion involved in cell communication / cell adhesive protein binding involved in bundle of His cell-Purkinje myocyte communication / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Harrison, O.J. / Brasch, J. / Shapiro, L. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of adhesive binding by desmocollins and desmogleins. Authors: Harrison, O.J. / Brasch, J. / Lasso, G. / Katsamba, P.S. / Ahlsen, G. / Honig, B. / Shapiro, L. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 354.4 KB | Display | ![]() |
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PDB format | ![]() | 291.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5eqxC ![]() 5erdSC ![]() 5iryC ![]() 5j5jC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 50331.996 Da / Num. of mol.: 2 / Fragment: unp residues 236-680 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Sugars , 3 types, 14 molecules ![](data/chem/img/MAN.gif)
![](data/chem/img/NAG.gif)
![](data/chem/img/NAG.gif)
#2: Polysaccharide | ![]() Source method: isolated from a genetically manipulated source #3: Sugar | ChemComp-MAN / ![]() #4: Sugar | ![]() |
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-Non-polymers , 4 types, 139 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-CA / #6: Chemical | ![]() #7: Chemical | ChemComp-EDO / ![]() #8: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.43 Å3/Da / Density % sol: 72.24 % |
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Crystal grow![]() | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 30% (w/v) EDO_P8K (Molecular Dimensions), 10% amino acids mix (Molecular Dimensions), 0.1M MES-imidazole pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 11, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.7→20 Å / Num. obs: 45932 / % possible obs: 98 % / Redundancy: 3.8 % / Net I/σ(I): 12.7 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 5ERD Resolution: 2.7→79.121 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.73 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→79.121 Å
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Refine LS restraints |
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LS refinement shell |
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