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Yorodumi- PDB-5ict: Crystal structure of the Drosophila GluR1A ligand binding domain ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ict | ||||||
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Title | Crystal structure of the Drosophila GluR1A ligand binding domain Y792T mutant complex with glutamate | ||||||
Components | Glutamate receptor 1 | ||||||
Keywords | MEMBRANE PROTEIN | ||||||
Function / homology | Function and homology information Activation of AMPA receptors / Trafficking of GluR2-containing AMPA receptors / Synaptic adhesion-like molecules / Unblocking of NMDA receptors, glutamate binding and activation / glutamate receptor activity / monoatomic cation transport / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential ...Activation of AMPA receptors / Trafficking of GluR2-containing AMPA receptors / Synaptic adhesion-like molecules / Unblocking of NMDA receptors, glutamate binding and activation / glutamate receptor activity / monoatomic cation transport / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / postsynaptic density membrane / modulation of chemical synaptic transmission / plasma membrane Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å | ||||||
Authors | Dharkar, P. / Mayer, M.L. | ||||||
Citation | Journal: Neuron / Year: 2016 Title: Novel Functional Properties of Drosophila CNS Glutamate Receptors. Authors: Li, Y. / Dharkar, P. / Han, T.H. / Serpe, M. / Lee, C.H. / Mayer, M.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ict.cif.gz | 175.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ict.ent.gz | 140.8 KB | Display | PDB format |
PDBx/mmJSON format | 5ict.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ict_validation.pdf.gz | 446.1 KB | Display | wwPDB validaton report |
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Full document | 5ict_full_validation.pdf.gz | 447.5 KB | Display | |
Data in XML | 5ict_validation.xml.gz | 14.9 KB | Display | |
Data in CIF | 5ict_validation.cif.gz | 22.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ic/5ict ftp://data.pdbj.org/pub/pdb/validation_reports/ic/5ict | HTTPS FTP |
-Related structure data
Related structure data | 5dt6SC 5dtbC 5ehmC 5ehsC 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: 30504.668 Da / Num. of mol.: 1 / Fragment: unp residues 474-594; unp residues 739-880 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: GluRIA, Glu-RI, CG8442 / Plasmid: pet22 / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B(DE3) / References: UniProt: Q03445 | ||
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#2: Chemical | ChemComp-GLU / | ||
#3: Chemical | #4: 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: 2.54 Å3/Da / Density % sol: 51.61 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: Sample buffer 150 NaCl, 10 Tris pH 8.5, 5 Na Glutamate, 1 mM EDTA, 10% glycerol Reservoir 12% PEG 8K, 100 Tris pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Feb 15, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.68→30 Å / Num. obs: 36199 / % possible obs: 98.9 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.031 / Net I/σ(I): 34.2 |
Reflection shell | Resolution: 1.68→1.71 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.8 / % possible all: 88.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5DT6 Resolution: 1.68→29.203 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 15.43
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.68→29.203 Å
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Refine LS restraints |
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LS refinement shell |
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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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