+Open data
-Basic information
Entry | Database: PDB / ID: 2byg | ||||||
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Title | 2nd PDZ Domain of Discs Large Homologue 2 | ||||||
Components | CHANNEL ASSOCIATED PROTEIN OF SYNAPSE-110 | ||||||
Keywords | SIGNAL TRANSDUCTION / DLG2 / PDZ / PDZ DOMAIN / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM / SGC / PHOSPHORYLATION / SH3 DOMAIN | ||||||
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 / perikaryon / chemical synaptic transmission / 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 / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Elkins, J.M. / Schoch, G.A. / Smee, C.E.A. / Berridge, G. / Salah, E. / Sundstrom, M. / Edwards, A. / Arrowsmith, C. / Weigelt, J. / 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, C. / Doyle, D.A. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2byg.cif.gz | 34.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2byg.ent.gz | 22.6 KB | Display | PDB format |
PDBx/mmJSON format | 2byg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/by/2byg ftp://data.pdbj.org/pub/pdb/validation_reports/by/2byg | HTTPS FTP |
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-Related structure data
Related structure data | 2fcfC 2fneC 2gzvC 2he2C 2he4C 2i1nC 2iwnC 2iwoC 2iwpC 2iwqC 1pdrS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 12787.502 Da / Num. of mol.: 1 / Fragment: 2ND PDZ DOMAIN, RESIDUES 190-283 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q15700 | ||
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#2: Water | ChemComp-HOH / | ||
Compound details | INTERACTS WITH THE CYTOPLASMISequence details | MUTATION RESIDUE ASN278 TO LYS A278 IS A CLONING ARTEFACT | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.6 % / Description: NONE |
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Crystal grow | pH: 8 / Details: 25% PEG 3350, 0.2M NACL, 0.1M BIS-TRIS PH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 |
Detector | Type: RIGAKU-MSC / Detector: IMAGE PLATE / Date: Jun 23, 2005 / Details: OSMIC MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→34.54 Å / Num. obs: 9967 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 19.9 |
Reflection shell | Resolution: 1.85→1.95 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.2 / % possible all: 91.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PDR Resolution: 1.85→50.51 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / SU B: 7.246 / SU ML: 0.117 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.141 / ESU R Free: 0.145 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.84 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→50.51 Å
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Refine LS restraints |
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