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Yorodumi- PDB-4u91: GephE in complex with Para-Phenyl crosslinked Glycine receptor be... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4u91 | |||||||||
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Title | GephE in complex with Para-Phenyl crosslinked Glycine receptor beta subunit derived dimeric peptide | |||||||||
Components |
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Keywords | TRANSFER PROTEIN / STRUCTURAL PROTEIN / Transferase / Scaffolding protein / Inhibitory synapse / GABA type A receptor / transfer protein - structural protein complex | |||||||||
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: 2 Å | |||||||||
Authors | Kasaragod, V.B. / Maric, H.M. / Schindelin, H. | |||||||||
Funding support | Germany, 1items
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Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2015 Title: Design and Synthesis of High-Affinity Dimeric Inhibitors Targeting the Interactions between Gephyrin and Inhibitory Neurotransmitter Receptors. Authors: Maric, H.M. / Kasaragod, V.B. / Haugaard-Kedstrom, L. / Hausrat, T.J. / Kneussel, M. / Schindelin, H. / Strmgaard, K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4u91.cif.gz | 187.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4u91.ent.gz | 148.1 KB | Display | PDB format |
PDBx/mmJSON format | 4u91.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4u91_validation.pdf.gz | 811.9 KB | Display | wwPDB validaton report |
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Full document | 4u91_full_validation.pdf.gz | 823.4 KB | Display | |
Data in XML | 4u91_validation.xml.gz | 22.4 KB | Display | |
Data in CIF | 4u91_validation.cif.gz | 32.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u9/4u91 ftp://data.pdbj.org/pub/pdb/validation_reports/u9/4u91 | HTTPS FTP |
-Related structure data
Related structure data | 4u90C 2fu3S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein / Protein/peptide , 2 types, 3 molecules ABE
#1: Protein | Mass: 45652.395 Da / Num. of mol.: 1 / Fragment: Gephyrin E domain, UNP Residues 344-762 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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#2: Protein/peptide | Mass: 1194.382 Da / Num. of mol.: 2 / Mutation: Additional Cysteine at the C terminus / Source method: obtained synthetically / Source: (synth.) Rattus norvegicus (Norway rat) |
-Non-polymers , 5 types, 292 molecules
#3: Chemical | ChemComp-ACT / |
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#4: Chemical | ChemComp-EDO / |
#5: Chemical | ChemComp-CA / |
#6: Chemical | ChemComp-3F7 / |
#7: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.56 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 0.2 M calcium acetate, 0.1M sodium acetate pH 4.5, 20-30% 2-methyl 2,4-pentanediol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 14, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2→56.2 Å / Num. obs: 33407 / % possible obs: 100 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.576 / Mean I/σ(I) obs: 2.5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2FU3 Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.941 / SU B: 8.705 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.157 / 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: 48.437 Å2
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Refinement step | Cycle: 1 / Resolution: 2→20 Å
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