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Open data
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Basic information
Entry | Database: PDB / ID: 5nxj | ||||||
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Title | SH3 domain from Mouse cortactin (P 1 21 1 crystal form) | ||||||
![]() | Src substrate cortactin | ||||||
![]() | PROTEIN BINDING / SH3 domain / cortactin / signaling / cancer / invadopodium | ||||||
Function / homology | ![]() lamellipodium organization / site of polarized growth / Arp2/3 complex binding / modification of postsynaptic actin cytoskeleton / modification of postsynaptic structure / mitotic spindle midzone / regulation of cell projection assembly / regulation of mitophagy / profilin binding / postsynaptic actin cytoskeleton ...lamellipodium organization / site of polarized growth / Arp2/3 complex binding / modification of postsynaptic actin cytoskeleton / modification of postsynaptic structure / mitotic spindle midzone / regulation of cell projection assembly / regulation of mitophagy / profilin binding / postsynaptic actin cytoskeleton / positive regulation of smooth muscle contraction / regulation of actin filament polymerization / positive regulation of chemotaxis / substrate-dependent cell migration, cell extension / focal adhesion assembly / podosome / proline-rich region binding / dendritic spine maintenance / regulation of axon extension / cortical actin cytoskeleton / positive regulation of actin filament polymerization / cortical cytoskeleton / extrinsic apoptotic signaling pathway / clathrin-coated pit / voltage-gated potassium channel complex / ruffle / receptor-mediated endocytosis / neuron projection morphogenesis / negative regulation of extrinsic apoptotic signaling pathway / actin filament / cell motility / intracellular protein transport / actin filament binding / cell migration / cell junction / lamellipodium / cell cortex / actin cytoskeleton organization / postsynapse / dendritic spine / focal adhesion / glutamatergic synapse / Golgi apparatus / endoplasmic reticulum / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Twafra, S. / Dessau, M. | ||||||
![]() | ![]() Title: SH3 domain from Mouse cortactin (P 1 21 1 crystal form) Authors: Twafra, S. / Gil-Henn, H. / Dessau, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 212.8 KB | Display | ![]() |
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PDB format | ![]() | 175.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1x69S 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: 6802.532 Da / Num. of mol.: 6 / Fragment: SH3 domain, UNP Residues 490-546 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.69 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 1.2 M (NH4)2SO4, 0.1 M sodium citrate pH 5, 3% 2_propanol |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 3, 2016 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.976251 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.28→60.257 Å / Num. obs: 17678 / % possible obs: 98.4 % / Redundancy: 3.368 % / Biso Wilson estimate: 30.11 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.163 / Rrim(I) all: 0.194 / Χ2: 0.94 / Net I/σ(I): 6.16 / Num. measured all: 59539 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1X69 Resolution: 2.282→60.257 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 27.59 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 144.53 Å2 / Biso mean: 40.7326 Å2 / Biso min: 15.75 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.282→60.257 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6
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Refinement TLS params. | Method: refined / Origin x: -17.9444 Å / Origin y: -11.1434 Å / Origin z: -14.7689 Å
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Refinement TLS group |
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