+Open data
-Basic information
Entry | Database: PDB / ID: 2i1n | ||||||
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Title | Crystal structure of the 1st PDZ domain of Human DLG3 | ||||||
Components | Discs, large homolog 3 | ||||||
Keywords | SIGNALING PROTEIN / DLG3 / PDZ / PDZ domain / signal transduction / structural genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information negative regulation of phosphatase activity / establishment of planar polarity / : / NrCAM interactions / receptor localization to synapse / structural constituent of postsynaptic density / Synaptic adhesion-like molecules / establishment or maintenance of epithelial cell apical/basal polarity / Assembly and cell surface presentation of NMDA receptors / Neurexins and neuroligins ...negative regulation of phosphatase activity / establishment of planar polarity / : / NrCAM interactions / receptor localization to synapse / structural constituent of postsynaptic density / Synaptic adhesion-like molecules / establishment or maintenance of epithelial cell apical/basal polarity / Assembly and cell surface presentation of NMDA receptors / Neurexins and neuroligins / Activation of Ca-permeable Kainate Receptor / receptor clustering / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / regulation of postsynaptic membrane neurotransmitter receptor levels / postsynaptic density, intracellular component / regulation of NMDA receptor activity / Long-term potentiation / AMPA glutamate receptor complex / bicellular tight junction / phosphatase binding / positive regulation of protein tyrosine kinase activity / ionotropic glutamate receptor binding / Ras activation upon Ca2+ influx through NMDA receptor / dendritic shaft / PDZ domain binding / postsynaptic density membrane / adherens junction / neuromuscular junction / cell-cell adhesion / kinase binding / MAPK cascade / cell junction / growth cone / chemical synaptic transmission / RAF/MAP kinase cascade / basolateral plasma membrane / protein phosphatase binding / neuron projection / negative regulation of cell population proliferation / neuronal cell body / glutamatergic synapse / ubiquitin protein ligase binding / extracellular space / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Turnbull, A.P. / Phillips, C. / Bunkoczi, G. / Debreczeni, J. / Ugochukwu, E. / Pike, A.C.W. / Gorrec, F. / Umeano, C. / Elkins, J. / Berridge, G. ...Turnbull, A.P. / Phillips, C. / Bunkoczi, G. / Debreczeni, J. / Ugochukwu, E. / Pike, A.C.W. / Gorrec, F. / Umeano, C. / Elkins, J. / Berridge, G. / Savitsky, P. / Gileadi, O. / von Delft, F. / Weigelt, J. / Edwards, A. / Arrowsmith, C. / Sundstrom, M. / Doyle, D. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Protein Sci. / Year: 2007 Title: Structure of PICK1 and other PDZ domains obtained with the help of self-binding C-terminal extensions. Authors: Elkins, J.M. / Papagrigoriou, E. / Berridge, G. / Yang, X. / Phillips, C. / Gileadi, C. / Savitsky, P. / Doyle, D.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2i1n.cif.gz | 56 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2i1n.ent.gz | 40.2 KB | Display | PDB format |
PDBx/mmJSON format | 2i1n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i1/2i1n ftp://data.pdbj.org/pub/pdb/validation_reports/i1/2i1n | HTTPS FTP |
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-Related structure data
Related structure data | 2bygC 2fcfC 2fneC 2gzvC 2he2C 2he4C 2iwnC 2iwoC 2iwpC 2iwqC 2fe5S 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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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 10931.439 Da / Num. of mol.: 2 / Fragment: PDZ1 domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DLG3 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)-R3 / References: UniProt: Q5JUW7, UniProt: Q92796*PLUS #2: Chemical | ChemComp-NA / #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: 2.55 Å3/Da / Density % sol: 51.74 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 1.0M LiSO4; 0.5M TMAO, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9791 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 12, 2006 |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→50 Å / Num. all: 19545 / Num. obs: 19545 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.85→1.92 Å / % possible all: 96.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID = 2FE5 Resolution: 1.85→29.16 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.945 / SU B: 5.292 / SU ML: 0.086 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.135 / ESU R Free: 0.125 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.313 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→29.16 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.898 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 |
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