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Yorodumi- PDB-6fgd: Crystal structure of Gephyrin E domain in complex with Artemether -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fgd | ||||||
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Title | Crystal structure of Gephyrin E domain in complex with Artemether | ||||||
Components | Gephyrin | ||||||
Keywords | STRUCTURAL PROTEIN / Antimalarial compound / scaffolding protein / moonlighting protein / inhibitory neurotransmission | ||||||
Function / homology | Function and homology information Molybdenum cofactor biosynthesis / molybdopterin cofactor biosynthetic process / glycine receptor clustering / molybdopterin adenylyltransferase / molybdopterin adenylyltransferase activity / establishment of synaptic specificity at neuromuscular junction / molybdopterin molybdotransferase / molybdopterin molybdotransferase activity / postsynaptic specialization / gamma-aminobutyric acid receptor clustering ...Molybdenum cofactor biosynthesis / molybdopterin cofactor biosynthetic process / glycine receptor clustering / molybdopterin adenylyltransferase / molybdopterin adenylyltransferase activity / establishment of synaptic specificity at neuromuscular junction / molybdopterin molybdotransferase / molybdopterin molybdotransferase activity / postsynaptic specialization / gamma-aminobutyric acid receptor clustering / nitrate reductase activity / inhibitory synapse / Mo-molybdopterin cofactor biosynthetic process / glycinergic synapse / postsynaptic neurotransmitter receptor diffusion trapping / response to metal ion / postsynaptic specialization membrane / molybdopterin cofactor binding / neurotransmitter receptor localization to postsynaptic specialization membrane / postsynaptic specialization, intracellular component / GABA-ergic synapse / protein targeting / synapse assembly / tubulin binding / synaptic membrane / establishment of protein localization / cytoplasmic side of plasma membrane / protein-macromolecule adaptor activity / postsynapse / postsynaptic membrane / molecular adaptor activity / postsynaptic density / cytoskeleton / signaling receptor binding / neuronal cell body / dendrite / ATP binding / identical protein binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Kasaragod, V.B. / Schindelin, H. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Neuron / Year: 2019 Title: Elucidating the Molecular Basis for Inhibitory Neurotransmission Regulation by Artemisinins. Authors: Kasaragod, V.B. / Hausrat, T.J. / Schaefer, N. / Kuhn, M. / Christensen, N.R. / Tessmer, I. / Maric, H.M. / Madsen, K.L. / Sotriffer, C. / Villmann, C. / Kneussel, M. / Schindelin, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fgd.cif.gz | 278.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fgd.ent.gz | 227.3 KB | Display | PDB format |
PDBx/mmJSON format | 6fgd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6fgd_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6fgd_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6fgd_validation.xml.gz | 23.5 KB | Display | |
Data in CIF | 6fgd_validation.cif.gz | 35.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fg/6fgd ftp://data.pdbj.org/pub/pdb/validation_reports/fg/6fgd | HTTPS FTP |
-Related structure data
Related structure data | 6fgcC 6hsnC 6hsoC 5errS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 45652.395 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gphn, Gph / Production host: Escherichia coli (E. coli) References: UniProt: Q03555, molybdopterin adenylyltransferase, molybdopterin molybdotransferase |
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-Non-polymers , 8 types, 455 molecules
#2: Chemical | #3: Chemical | ChemComp-PO4 / | #4: Chemical | ChemComp-ACT / #5: Chemical | ChemComp-NA / | #6: Chemical | ChemComp-ADP / | #7: Chemical | ChemComp-MPD / ( | #8: Chemical | ChemComp-D8Z / | #9: 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: 2.66 Å3/Da / Density % sol: 53.71 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 0.1 M sodium acetate 20-36% MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9762 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 24, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→43.58 Å / Num. obs: 77361 / % possible obs: 99.5 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.051 / Rrim(I) all: 0.096 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 1.5→1.53 Å / Rmerge(I) obs: 1.284 / Rpim(I) all: 0.816 / Rrim(I) all: 1.527 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5ERR Resolution: 1.5→43.58 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.02 / 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: 1.5→43.58 Å
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Refine LS restraints |
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LS refinement shell |
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