+Open data
-Basic information
Entry | Database: PDB / ID: 5nxj | ||||||
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Title | SH3 domain from Mouse cortactin (P 1 21 1 crystal form) | ||||||
Components | Src substrate cortactin | ||||||
Keywords | PROTEIN BINDING / SH3 domain / cortactin / signaling / cancer / invadopodium | ||||||
Function / homology | Function and homology information 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 / profilin binding / substrate-dependent cell migration, cell extension / 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 / profilin binding / substrate-dependent cell migration, cell extension / postsynaptic actin cytoskeleton / regulation of autophagy of mitochondrion / positive regulation of smooth muscle contraction / positive regulation of chemotaxis / regulation of actin filament polymerization / focal adhesion assembly / podosome / regulation of axon extension / proline-rich region binding / dendritic spine maintenance / cortical actin cytoskeleton / cortical cytoskeleton / positive regulation of actin filament polymerization / voltage-gated potassium channel complex / extrinsic apoptotic signaling pathway / clathrin-coated pit / ruffle / receptor-mediated endocytosis / neuron projection morphogenesis / cell motility / actin filament / negative regulation of extrinsic apoptotic signaling pathway / intracellular protein transport / actin filament binding / lamellipodium / cell junction / cell cortex / actin cytoskeleton organization / postsynapse / dendritic spine / focal adhesion / intracellular membrane-bounded organelle / glutamatergic synapse / Golgi apparatus / endoplasmic reticulum / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.282 Å | ||||||
Authors | Twafra, S. / Dessau, M. | ||||||
Citation | Journal: To Be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5nxj.cif.gz | 212.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nxj.ent.gz | 175.3 KB | Display | PDB format |
PDBx/mmJSON format | 5nxj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nx/5nxj ftp://data.pdbj.org/pub/pdb/validation_reports/nx/5nxj | 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 |
-Links
-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.) Mus musculus (house mouse) / Gene: Cttn, Ems1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q60598 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.976251 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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