+Open data
-Basic information
Entry | Database: PDB / ID: 5szn | ||||||||||||
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Title | Protocadherin gamma A9 extracellular cadherin domains 1-5 | ||||||||||||
Components | Protocadherin gamma A9 | ||||||||||||
Keywords | CELL ADHESION | ||||||||||||
Function / homology | Function and homology information homophilic cell adhesion via plasma membrane adhesion molecules / plasma membrane => GO:0005886 / spermatogenesis / cell adhesion / calcium ion binding / membrane Similarity search - Function | ||||||||||||
Biological species | Mus musculus (house mouse) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.944 Å | ||||||||||||
Authors | Goodman, K.M. / Mannepalli, S. / Bahna, F. / Honig, B. / Shapiro, L. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Elife / Year: 2016 Title: gamma-Protocadherin structural diversity and functional implications. Authors: Goodman, K.M. / Rubinstein, R. / Thu, C.A. / Mannepalli, S. / Bahna, F. / Ahlsen, G. / Rittenhouse, C. / Maniatis, T. / Honig, B. / Shapiro, L. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5szn.cif.gz | 225 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5szn.ent.gz | 178.3 KB | Display | PDB format |
PDBx/mmJSON format | 5szn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sz/5szn ftp://data.pdbj.org/pub/pdb/validation_reports/sz/5szn | HTTPS FTP |
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-Related structure data
Related structure data | 5szlC 5szmC 5szoC 5szpC 5szqC 5szrC 5t9tC 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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 59634.922 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Extracellular cadherin domains 1-5 of PcdhgA9 with a C-terminal octahistidine tag. Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pcdhga9 / Production host: Homo sapiens (human) / References: UniProt: Q91XX9 |
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-Sugars , 3 types, 5 molecules
#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 | ||
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#3: Sugar | #4: Sugar | ChemComp-NAG / | |
-Non-polymers , 3 types, 54 molecules
#5: Chemical | ChemComp-CA / #6: Chemical | #7: Water | ChemComp-HOH / | |
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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: 4.28 Å3/Da / Density % sol: 71.25 % |
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Crystal grow | Temperature: 295 K / Method: batch mode / pH: 6.5 Details: 10% (w/v) PEG4000, 20% (v/v) glycerol, 30 mM magnesium chloride, 30 mM calcium chloride, 0.1 M Morpheus Buffer System 1 (Mes/Imidazole buffer; Molecular Dimensions) pH 6.5 |
-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: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 26, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.94→40 Å / Num. obs: 13469 / % possible obs: 98.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 53.84 Å2 / Rmerge(I) obs: 0.229 / Net I/σ(I): 4.5 |
Reflection shell | Resolution: 2.94→3.12 Å / Redundancy: 3.8 % / Rmerge(I) obs: 3.156 / Mean I/σ(I) obs: 0.6 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PCDHGA8 Resolution: 2.944→19.996 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 37.9 / 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: 2.944→19.996 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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