+Open data
-Basic information
Entry | Database: PDB / ID: 4mt6 | ||||||
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Title | Crystal structure of closed inactive collybistin | ||||||
Components | Rho guanine nucleotide exchange factor 9 | ||||||
Keywords | PROTEIN BINDING / closed conformation | ||||||
Function / homology | Function and homology information CDC42 GTPase cycle / GABA receptor activation / regulation of postsynaptic specialization assembly / NRAGE signals death through JNK / G alpha (12/13) signalling events / RHOQ GTPase cycle / postsynaptic specialization / glycinergic synapse / receptor clustering / GABA-ergic synapse ...CDC42 GTPase cycle / GABA receptor activation / regulation of postsynaptic specialization assembly / NRAGE signals death through JNK / G alpha (12/13) signalling events / RHOQ GTPase cycle / postsynaptic specialization / glycinergic synapse / receptor clustering / GABA-ergic synapse / guanyl-nucleotide exchange factor activity / cell cortex / postsynaptic density / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 5.501 Å | ||||||
Authors | Schneeberger, D. / Schindelin, H. | ||||||
Citation | Journal: Embo J. / Year: 2014 Title: A conformational switch in collybistin determines the differentiation of inhibitory postsynapses. Authors: Soykan, T. / Schneeberger, D. / Tria, G. / Buechner, C. / Bader, N. / Svergun, D. / Tessmer, I. / Poulopoulos, A. / Papadopoulos, T. / Varoqueaux, F. / Schindelin, H. / Brose, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4mt6.cif.gz | 182.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mt6.ent.gz | 149 KB | Display | PDB format |
PDBx/mmJSON format | 4mt6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mt/4mt6 ftp://data.pdbj.org/pub/pdb/validation_reports/mt/4mt6 | HTTPS FTP |
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-Related 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: 54078.262 Da / Num. of mol.: 1 / Mutation: G33E, V34L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Arhgef9 / Plasmid: pTYB12 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9QX73 |
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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: 7.9 Å3/Da / Density % sol: 84.43 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 20mM Na-cacodylate, 5mM Co(III)hexamine chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 77 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 23, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: horizontally diffracting Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 5.501→153.625 Å / Num. all: 5698 / Num. obs: 5698 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11 % / Biso Wilson estimate: 300.13 Å2 / Rsym value: 0.155 / Net I/σ(I): 10.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 5.501→108.629 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.91 / σ(F): 1.35 / Phase error: 38.44 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 177.0586 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 5.501→108.629 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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