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Open data
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Basic information
Entry | Database: PDB / ID: 4zpl | |||||||||
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Title | Crystal Structure of Protocadherin Beta 1 EC1-3 | |||||||||
![]() | Protein Pcdhb1 | |||||||||
![]() | CELL ADHESION | |||||||||
Function / homology | ![]() homophilic cell adhesion via plasma membrane adhesion molecules / plasma membrane => GO:0005886 / cell adhesion / calcium ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Goodman, K.M. / Bahna, F. / Shapiro, L. | |||||||||
![]() | ![]() Title: Molecular Logic of Neuronal Self-Recognition through Protocadherin Domain Interactions. Authors: Rubinstein, R. / Thu, C.A. / Goodman, K.M. / Wolcott, H.N. / Bahna, F. / Mannepalli, S. / Ahlsen, G. / Chevee, M. / Halim, A. / Clausen, H. / Maniatis, T. / Shapiro, L. / Honig, B. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 142.8 KB | Display | ![]() |
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PDB format | ![]() | 111.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4zpmC ![]() 4zpnC ![]() 4zpoSC ![]() 4zppC ![]() 4zpqC ![]() 4zpsC 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
#1: Protein | Mass: 35757.066 Da / Num. of mol.: 1 / Fragment: UNP residues 29-342 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Chemical | ChemComp-CA / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.17 Å3/Da / Density % sol: 70.51 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 24% (w/v) PEG1500, 20% (v/v) glycerol, 3% (w/v) glucose |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 23, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→41.7 Å / Num. obs: 9021 / % possible obs: 97.9 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 4.6 |
Reflection shell | Resolution: 3.3→3.56 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 1.6 / % possible all: 97.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4ZPO Resolution: 3.3→41.696 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.97 / 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: 3.3→41.696 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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