+Open data
-Basic information
Entry | Database: PDB / ID: 2ydl | ||||||
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Title | Crystal structure of SH3C from CIN85 | ||||||
Components | SH3 DOMAIN-CONTAINING KINASE-BINDING PROTEIN 1 | ||||||
Keywords | SIGNALING PROTEIN | ||||||
Function / homology | Function and homology information Reelin signalling pathway / positive regulation of B cell activation / endocytic vesicle / cytoskeleton organization / InlB-mediated entry of Listeria monocytogenes into host cell / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / actin filament organization / EGFR downregulation / cytoplasmic vesicle membrane / Negative regulation of MET activity ...Reelin signalling pathway / positive regulation of B cell activation / endocytic vesicle / cytoskeleton organization / InlB-mediated entry of Listeria monocytogenes into host cell / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / actin filament organization / EGFR downregulation / cytoplasmic vesicle membrane / Negative regulation of MET activity / SH3 domain binding / endocytosis / cell-cell junction / cell migration / Cargo recognition for clathrin-mediated endocytosis / cell-cell signaling / Clathrin-mediated endocytosis / regulation of cell shape / Potential therapeutics for SARS / cytoskeleton / neuron projection / focal adhesion / apoptotic process / ubiquitin protein ligase binding / synapse / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Bravo, J. / Cardenes, N. | ||||||
Citation | Journal: Plos One / Year: 2013 Title: Distinct Ubiquitin Binding Modes Exhibited by SH3 Domains: Molecular Determinants and Functional Implications. Authors: Ortega Roldan, J.L. / Casares, S. / Ringkjobing Jensen, M. / Cardenes, N. / Bravo, J. / Blackledge, M. / Azuaga, A.I. / Van Nuland, N.A.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ydl.cif.gz | 26.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ydl.ent.gz | 16.8 KB | Display | PDB format |
PDBx/mmJSON format | 2ydl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ydl_validation.pdf.gz | 420 KB | Display | wwPDB validaton report |
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Full document | 2ydl_full_validation.pdf.gz | 420.2 KB | Display | |
Data in XML | 2ydl_validation.xml.gz | 5.5 KB | Display | |
Data in CIF | 2ydl_validation.cif.gz | 6.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yd/2ydl ftp://data.pdbj.org/pub/pdb/validation_reports/yd/2ydl | HTTPS FTP |
-Related structure data
Related structure data | 2lz6C 2mcnC 1semS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 8034.963 Da / Num. of mol.: 1 / Fragment: SH3 C, RESIDUES 270-328 Source method: isolated from a genetically manipulated source Details: THIRD SH3 DOMAIN / Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q96B97 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 59 % / Description: NONE |
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Crystal grow | Details: 0.1M CITRATE PH 5.5, 2.0 M AMMONIUM SULPHATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER FR530 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 4, 2007 / Details: MIRROR |
Radiation | Monochromator: NI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→26.78 Å / Num. obs: 5991 / % possible obs: 95.4 % / Observed criterion σ(I): 6 / Redundancy: 3.13 % / Rmerge(I) obs: 0.28 / Net I/σ(I): 8.31 |
Reflection shell | Resolution: 2.03→2.14 Å / Redundancy: 3.13 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 3.2 / % possible all: 82.3 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1SEM Resolution: 2.05→41.42 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.912 / SU B: 4.67 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.791 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→41.42 Å
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