+Open data
-Basic information
Entry | Database: PDB / ID: 5szm | ||||||||||||
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Title | Protocadherin gamma A8 extracellular cadherin domains 1-4 | ||||||||||||
Components | PcdhgA8 or protocadherin gamma A8 | ||||||||||||
Keywords | CELL ADHESION | ||||||||||||
Function / homology | Function and homology information homophilic cell adhesion via plasma membrane adhesion molecules / cell adhesion / calcium ion binding / membrane / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Mus musculus (house mouse) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 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 | 5szm.cif.gz | 189.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5szm.ent.gz | 150 KB | Display | PDB format |
PDBx/mmJSON format | 5szm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5szm_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 5szm_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 5szm_validation.xml.gz | 17.2 KB | Display | |
Data in CIF | 5szm_validation.cif.gz | 22.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sz/5szm ftp://data.pdbj.org/pub/pdb/validation_reports/sz/5szm | HTTPS FTP |
-Related structure data
Related structure data | 5szlC 5sznC 5szoC 5szpC 5szqC 5szrC 5t9tC 4zpsS C: citing same article (ref.) S: Starting model for refinement |
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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: 47545.051 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pcdhga8, mCG_133388 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q91XY0 | ||
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#2: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]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 | ||
#4: Chemical | ChemComp-CA / #5: Sugar | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 9.17 Å3/Da / Density % sol: 86.59 % / Description: Rod |
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Crystal grow | Temperature: 295 K / Method: batch mode / pH: 7.5 Details: 11% isopropanol, 50 mM sodium chloride, 0.1 M Hepes pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97915 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 14, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 3.6→66.51 Å / Num. obs: 20729 / % possible obs: 99.8 % / Redundancy: 7.1 % / Biso Wilson estimate: 104.64 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.172 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 3.6→3.97 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.913 / Mean I/σ(I) obs: 2.3 / CC1/2: 0.864 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ZPS Resolution: 3.6→19.938 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.29 / 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: 3.6→19.938 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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