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Yorodumi- PDB-4rp4: Crystal Structure of the L27 domain of Discs Large 1 (target ID N... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4rp4 | ||||||
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Title | Crystal Structure of the L27 domain of Discs Large 1 (target ID NYSGRC-010766) from Drosophila melanogaster (space group P212121) | ||||||
Components | Disks large 1 tumor suppressor protein | ||||||
Keywords | ANTITUMOR PROTEIN / NYSGRC / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / Scaffolding | ||||||
Function / homology | Function and homology information smooth septate junction / positive phototaxis / RHO GTPases activate CIT / Neurexins and neuroligins / establishment or maintenance of polarity of larval imaginal disc epithelium / cell fate commitment involved in pattern specification / type I terminal bouton / septate junction / septate junction assembly / negative regulation of imaginal disc growth ...smooth septate junction / positive phototaxis / RHO GTPases activate CIT / Neurexins and neuroligins / establishment or maintenance of polarity of larval imaginal disc epithelium / cell fate commitment involved in pattern specification / type I terminal bouton / septate junction / septate junction assembly / negative regulation of imaginal disc growth / Activation of Ca-permeable Kainate Receptor / morphogenesis of follicular epithelium / type Ib terminal bouton / subsynaptic reticulum / Synaptic adhesion-like molecules / establishment or maintenance of polarity of follicular epithelium / morphogenesis of larval imaginal disc epithelium / Unblocking of NMDA receptors, glutamate binding and activation / gravitaxis / tricellular tight junction / establishment of spindle orientation / anterior/posterior axis specification, follicular epithelium / negative regulation of peptidoglycan recognition protein signaling pathway / pole plasm protein localization / basal protein localization / asymmetric protein localization involved in cell fate determination / dorsal closure / follicle cell of egg chamber development / regulation of epidermal growth factor receptor signaling pathway / positive regulation of synaptic assembly at neuromuscular junction / male courtship behavior / guanylate kinase activity / morphogenesis of a polarized epithelium / behavioral response to ethanol / receptor localization to synapse / apical cortex / leading edge membrane / apicolateral plasma membrane / synaptic assembly at neuromuscular junction / establishment or maintenance of epithelial cell apical/basal polarity / mating behavior / cell fate specification / receptor clustering / locomotor rhythm / establishment of mitotic spindle orientation / lateral plasma membrane / postsynaptic density membrane / neuromuscular junction / terminal bouton / kinase binding / cell-cell adhesion / nervous system development / cell cortex / chemical synaptic transmission / basolateral plasma membrane / postsynaptic membrane / cytoskeleton / neuron projection / synapse / perinuclear region of cytoplasm / signal transduction / plasma membrane Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å | ||||||
Authors | Ghosh, A. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC) | ||||||
Citation | Journal: Biochemistry / Year: 2018 Title: Structures of the L27 Domain of Disc Large Homologue 1 Protein Illustrate a Self-Assembly Module. Authors: Ghosh, A. / Ramagopal, U.A. / Bonanno, J.B. / Brenowitz, M. / Almo, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4rp4.cif.gz | 98.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rp4.ent.gz | 75.2 KB | Display | PDB format |
PDBx/mmJSON format | 4rp4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4rp4_validation.pdf.gz | 442.2 KB | Display | wwPDB validaton report |
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Full document | 4rp4_full_validation.pdf.gz | 442.4 KB | Display | |
Data in XML | 4rp4_validation.xml.gz | 11 KB | Display | |
Data in CIF | 4rp4_validation.cif.gz | 15.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rp/4rp4 ftp://data.pdbj.org/pub/pdb/validation_reports/rp/4rp4 | HTTPS FTP |
-Related structure data
Related structure data | 4rp3SC 4rp5C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 11432.120 Da / Num. of mol.: 2 / Fragment: L27 domain residues 1-97 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CG1725, Discs Large 1 Isoform B, dlg1, l(1)dlg1 / Plasmid: pSGC-His / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) pRIL / References: UniProt: P31007 #2: Chemical | ChemComp-FMT / | #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: 1.96 Å3/Da / Density % sol: 37.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 10.5 Details: 0.2 M Sodium Format, 20 % PEG 3350, 3 % 1,8-Diaminooctane, pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 77 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 5, 2013 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: ROSENBAUM-ROCK DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.42→30 Å / Num. all: 35614 / Num. obs: 33288 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15 % / Rmerge(I) obs: 0.095 / Χ2: 1.15 / Net I/σ(I): 15.9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4RP3 Resolution: 1.42→28.21 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.316 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.071 / ESU R Free: 0.068 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 126.06 Å2 / Biso mean: 27.398 Å2 / Biso min: 12.57 Å2
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Refinement step | Cycle: LAST / Resolution: 1.42→28.21 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.42→1.454 Å / Total num. of bins used: 20
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Refinement TLS params. | L11: 0 °2 / L12: 0 °2 / L13: 0 °2 / L22: 0 °2 / L23: 0 °2 / L33: 0 °2 / S11: 0 Å ° / S12: 0 Å ° / S13: 0 Å ° / S21: 0 Å ° / S22: 0 Å ° / S23: 0 Å ° / S31: 0 Å ° / S32: 0 Å ° / S33: 0 Å ° / T11: 0 Å2 / T12: 0 Å2 / T13: 0 Å2 / T22: 0 Å2 / T23: 0 Å2 / T33: 0 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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