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Open data
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Basic information
Entry | Database: PDB / ID: 2a4e | ||||||
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Title | Crystal structure of mouse cadherin-11 EC1-2 | ||||||
![]() | Cadherin-11 | ||||||
![]() | CELL ADHESION / cadherin / dimer / calcium binding | ||||||
Function / homology | ![]() Regulation of CDH11 function / corticospinal tract morphogenesis / Adherens junctions interactions / cell-cell adhesion mediated by cadherin / cell-cell adhesion via plasma-membrane adhesion molecules / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / focal adhesion assembly / catenin complex / cell-cell junction assembly / adherens junction organization ...Regulation of CDH11 function / corticospinal tract morphogenesis / Adherens junctions interactions / cell-cell adhesion mediated by cadherin / cell-cell adhesion via plasma-membrane adhesion molecules / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / focal adhesion assembly / catenin complex / cell-cell junction assembly / adherens junction organization / homophilic cell adhesion via plasma membrane adhesion molecules / negative regulation of cell migration / adherens junction / Schaffer collateral - CA1 synapse / modulation of chemical synaptic transmission / cell morphogenesis / cell adhesion / cadherin binding / glutamatergic synapse / synapse / calcium ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Patel, S.D. / Ciatto, C. / Chen, C.P. / Bahna, F. / Arkus, N. / Rajebhosale, M. / Jessell, T.M. / Honig, B. / Price, S.R. / Shapiro, L. | ||||||
![]() | ![]() Title: Type II cadherin ectodomain structures: implications for classical cadherin specificity. Authors: Patel, S.D. / Ciatto, C. / Chen, C.P. / Bahna, F. / Rajebhosale, M. / Arkus, N. / Schieren, I. / Jessell, T.M. / Honig, B. / Price, S.R. / 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 | ![]() | 56 KB | Display | ![]() |
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PDB format | ![]() | 39.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 429.7 KB | Display | ![]() |
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Full document | ![]() | 436.5 KB | Display | |
Data in XML | ![]() | 10.5 KB | Display | |
Data in CIF | ![]() | 13.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1zvnSC ![]() 1zxkSC ![]() 2a4cC ![]() 2a62C ![]() 1edhS ![]() 1l3wS ![]() 1ncjS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 23787.211 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.37 Å3/Da / Density % sol: 77.08 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: ammonium sulfate, hepes, sucrose, calcium chloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→30 Å / Num. obs: 8610 / % possible obs: 99.9 % |
Reflection shell | Resolution: 3.2→3.31 Å / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1ZVN and 1ZXK for the EC1 domain, and the EC2 domains of PDB entries 1NCJ, 1EDH, and 1L3W, for the EC2 domain. Resolution: 3.2→30 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.907 / SU B: 31.513 / SU ML: 0.267 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.621 / ESU R Free: 0.352 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 74.397 Å2
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Refinement step | Cycle: LAST / Resolution: 3.2→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.278 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A
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