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- PDB-5l5g: Plexin A2 full extracellular region, domains 1 to 8 modeled, data... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5l5g | ||||||
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Title | Plexin A2 full extracellular region, domains 1 to 8 modeled, data to 10 angstrom | ||||||
![]() | Plexin-A2 | ||||||
![]() | SIGNALING PROTEIN / receptor / signaling / axon guidance | ||||||
Function / homology | ![]() cerebellar granule cell precursor tangential migration / CRMPs in Sema3A signaling / Sema3A PAK dependent Axon repulsion / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / limb bud formation / pharyngeal system development / semaphorin-plexin signaling pathway involved in axon guidance / semaphorin receptor activity / negative regulation of cell adhesion / semaphorin receptor complex ...cerebellar granule cell precursor tangential migration / CRMPs in Sema3A signaling / Sema3A PAK dependent Axon repulsion / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / limb bud formation / pharyngeal system development / semaphorin-plexin signaling pathway involved in axon guidance / semaphorin receptor activity / negative regulation of cell adhesion / semaphorin receptor complex / neural tube development / centrosome localization / positive regulation of axonogenesis / semaphorin-plexin signaling pathway / somitogenesis / regulation of cell migration / regulation of cell shape / collagen-containing extracellular matrix / cell surface receptor signaling pathway / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Janssen, B.J.C. / Kong, Y. / Malinauskas, T. / Vangoor, V.R. / Coles, C.H. / Kaufmann, R. / Ni, T. / Gilbert, R.J.C. / Padilla-Parra, S. / Pasterkamp, R.J. / Jones, E.Y. | ||||||
![]() | ![]() Title: Structural Basis for Plexin Activation and Regulation. Authors: Kong, Y. / Janssen, B.J. / Malinauskas, T. / Vangoor, V.R. / Coles, C.H. / Kaufmann, R. / Ni, T. / Gilbert, R.J. / Padilla-Parra, S. / Pasterkamp, R.J. / Jones, E.Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 654.6 KB | Display | ![]() |
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PDB format | ![]() | 498.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 464.9 KB | Display | ![]() |
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Full document | ![]() | 608 KB | Display | |
Data in XML | ![]() | 91.5 KB | Display | |
Data in CIF | ![]() | 133 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5l56C ![]() 5l59C ![]() 5l5cC ![]() 5l5kC ![]() 5l5lC ![]() 5l5mC ![]() 5l5nC ![]() 5l74C ![]() 5l7nC ![]() 3oktS 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 133579.266 Da / Num. of mol.: 4 / Fragment: UNP residues 33-1231 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density % sol: 85 % |
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Crystal grow | Temperature: 293.5 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.68 M potassium/sodium tartrate, 85 mM HEPES, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 26, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97922 Å / Relative weight: 1 |
Reflection | Resolution: 10→63.055 Å / Num. obs: 11079 / % possible obs: 93.9 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.187 / Net I/σ(I): 5.1 |
Reflection shell | Highest resolution: 10 Å / Rmerge(I) obs: 0.882 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3OKT Resolution: 10→63.055 Å / SU ML: 1.75 / Cross valid method: FREE R-VALUE / σ(F): 0.69 / Phase error: 41.78 Details: THE AUTHORS STATE THAT DUE TO THE LOW RESOLUTION OF THE DIFFRACTION DATA THE STRUCTURE WAS ONLY SUBJECTED TO RIGID BODY REFINEMENT WITH EACH DOMAIN AS RIGID BODY. THE STRUCTURE IS BASED ON ...Details: THE AUTHORS STATE THAT DUE TO THE LOW RESOLUTION OF THE DIFFRACTION DATA THE STRUCTURE WAS ONLY SUBJECTED TO RIGID BODY REFINEMENT WITH EACH DOMAIN AS RIGID BODY. THE STRUCTURE IS BASED ON PDB ENTRIES 3OKT AND 5L56. THE AUTHORS HAVE NOT FURTHER REFINED THE RESULTING COORDINATES NOR CORRECTED RESULTING CLASHES BETWEEN ATOMS AND DEVIATING PEPTIDE LINKAGES BETWEEN DOMAINS.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 10→63.055 Å
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Refine LS restraints |
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LS refinement shell |
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