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- PDB-5ehm: Crystal structure of the Drosophila CG3822 KaiR1D ligand binding ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ehm | |||||||||
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Title | Crystal structure of the Drosophila CG3822 KaiR1D ligand binding domain complex with NMDA | |||||||||
![]() | RE06730p,CG3822 | |||||||||
![]() | MEMBRANE PROTEIN | |||||||||
Function / homology | ![]() Activation of Na-permeable kainate receptors / Activation of Ca-permeable Kainate Receptor / positive regulation of glutamate secretion, neurotransmission / regulation of synaptic activity / positive regulation of neuromuscular synaptic transmission / glutamate receptor activity / glutamate-gated calcium ion channel activity / presynaptic active zone / kainate selective glutamate receptor activity / calcium ion import across plasma membrane ...Activation of Na-permeable kainate receptors / Activation of Ca-permeable Kainate Receptor / positive regulation of glutamate secretion, neurotransmission / regulation of synaptic activity / positive regulation of neuromuscular synaptic transmission / glutamate receptor activity / glutamate-gated calcium ion channel activity / presynaptic active zone / kainate selective glutamate receptor activity / calcium ion import across plasma membrane / presynaptic modulation of chemical synaptic transmission / positive regulation of synaptic transmission, glutamatergic / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / postsynaptic density membrane / modulation of chemical synaptic transmission / presynaptic membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Dharkar, P. / Mayer, M.L. | |||||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 329 KB | Display | ![]() |
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PDB format | ![]() | 272.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 454 KB | Display | ![]() |
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Full document | ![]() | 458.9 KB | Display | |
Data in XML | ![]() | 30.2 KB | Display | |
Data in CIF | ![]() | 47.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5dt6C ![]() 5dtbSC ![]() 5ehsC ![]() 5ictC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 29836.039 Da / Num. of mol.: 2 / Fragment: unp residues 411-529, unp residues 650-794 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 45 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: Buffer 150 NaCl 10 HEPES pH 7.5 20 mM NMDA 2 mM EDTA Reservoir 22% PEG 6K 0.1 M Na Acetate 0.1M Ammonium Sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Oct 23, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.28→40 Å / Num. obs: 134785 / % possible obs: 96.2 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.035 / Net I/σ(I): 49.44 |
Reflection shell | Resolution: 1.28→1.3 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 5.5 / % possible all: 70.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5DTB Resolution: 1.281→24.81 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0.07 / Phase error: 19.25 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.281→24.81 Å
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Refine LS restraints |
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LS refinement shell |
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