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Yorodumi- PDB-2he2: Crystal structure of the 3rd PDZ domain of human discs large homo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2he2 | ||||||
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Title | Crystal structure of the 3rd PDZ domain of human discs large homologue 2, DLG2 | ||||||
Components | Discs large homolog 2 | ||||||
Keywords | SIGNALING PROTEIN / DLG2 / PDZ / PDZ domain / signal transduction / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information retrograde axonal protein transport / anterograde axonal protein transport / guanylate kinase activity / receptor localization to synapse / cellular response to potassium ion / juxtaparanode region of axon / establishment or maintenance of epithelial cell apical/basal polarity / Assembly and cell surface presentation of NMDA receptors / Neurexins and neuroligins / receptor clustering ...retrograde axonal protein transport / anterograde axonal protein transport / guanylate kinase activity / receptor localization to synapse / cellular response to potassium ion / juxtaparanode region of axon / establishment or maintenance of epithelial cell apical/basal polarity / Assembly and cell surface presentation of NMDA receptors / Neurexins and neuroligins / receptor clustering / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / Long-term potentiation / axon cytoplasm / Ras activation upon Ca2+ influx through NMDA receptor / postsynaptic density membrane / adherens junction / neuromuscular junction / cell-cell adhesion / kinase binding / chemical synaptic transmission / perikaryon / RAF/MAP kinase cascade / basolateral plasma membrane / postsynaptic density / neuron projection / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Turnbull, A.P. / Phillips, C. / Berridge, G. / Savitsky, P. / Smee, C.E.A. / Papagrigoriou, E. / Debreczeni, J. / Gorrec, F. / Elkins, J.M. / von Delft, F. ...Turnbull, A.P. / Phillips, C. / Berridge, G. / Savitsky, P. / Smee, C.E.A. / Papagrigoriou, E. / Debreczeni, J. / Gorrec, F. / Elkins, J.M. / von Delft, F. / Weigelt, J. / Edwards, A. / Arrowsmith, C. / Sundstrom, M. / Doyle, D.A. / 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 | 2he2.cif.gz | 103.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2he2.ent.gz | 80.3 KB | Display | PDB format |
PDBx/mmJSON format | 2he2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/he/2he2 ftp://data.pdbj.org/pub/pdb/validation_reports/he/2he2 | HTTPS FTP |
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-Related structure data
Related structure data | 2bygC 2fcfC 2fneC 2gzvC 2he4C 2i1nC 2iwnC 2iwoC 2iwpC 2iwqC 1be9S 1bfeS 1tp3S 1tp5S 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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Unit cell |
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-Components
#1: Protein | Mass: 10676.890 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DLG2 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3/Rosetta / References: UniProt: Q15700 #2: 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: 2.23 Å3/Da / Density % sol: 44.81 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 25.5% PEG 3350; 0.17M (NH4)2SO4; 15% glycerol , 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: 0.97646 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 6, 2006 |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97646 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 30918 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.5→1.55 Å / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Swissmodel based upon the coordinates of pdb entries 1TP5, 1TP3, 1BFE and 1BE9. Resolution: 1.5→41.13 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.477 / SU ML: 0.043 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.077 / ESU R Free: 0.073 / 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: 9.045 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→41.13 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
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