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Yorodumi- PDB-1kjt: Crystal Structure of the GABA(A) Receptor Associated Protein, GABARAP -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kjt | ||||||
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Title | Crystal Structure of the GABA(A) Receptor Associated Protein, GABARAP | ||||||
Components | GABARAP | ||||||
Keywords | TRANSPORT PROTEIN / ubiquitin-like fold / N-terminal alpha helical region | ||||||
Function / homology | Function and homology information TBC/RABGAPs / Macroautophagy / autophagy of mitochondrion / GABA receptor binding / cellular response to nitrogen starvation / microtubule associated complex / beta-tubulin binding / axoneme / autophagosome membrane / autophagosome assembly ...TBC/RABGAPs / Macroautophagy / autophagy of mitochondrion / GABA receptor binding / cellular response to nitrogen starvation / microtubule associated complex / beta-tubulin binding / axoneme / autophagosome membrane / autophagosome assembly / extrinsic apoptotic signaling pathway via death domain receptors / smooth endoplasmic reticulum / autophagosome / sperm midpiece / macroautophagy / microtubule cytoskeleton organization / actin cytoskeleton / protein transport / cell body / cytoplasmic vesicle / microtubule binding / microtubule / lysosome / Golgi membrane / ubiquitin protein ligase binding / perinuclear region of cytoplasm / Golgi apparatus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Bavro, V.N. / Sola, M. / Bracher, A. / Kneussel, M. / Betz, H. / Weissenhorn, W. | ||||||
Citation | Journal: EMBO Rep. / Year: 2002 Title: Crystal structure of the GABA(A)-receptor-associated protein, GABARAP. Authors: Bavro, V.N. / Sola, M. / Bracher, A. / Kneussel, M. / Betz, H. / Weissenhorn, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kjt.cif.gz | 37.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kjt.ent.gz | 25.6 KB | Display | PDB format |
PDBx/mmJSON format | 1kjt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kj/1kjt ftp://data.pdbj.org/pub/pdb/validation_reports/kj/1kjt | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14100.201 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: modified pMAL-c2g / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 codon + / References: UniProt: P60517 | ||||
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#2: Chemical | #3: Chemical | ChemComp-NA / | #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: 1.92 Å3/Da / Density % sol: 35.88 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG 2000MME, Tris HCL, nickel chloride, sodium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.2 / Method: vapor diffusion | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.9333 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 20, 2001 |
Radiation | Monochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9333 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. all: 7790 / Num. obs: 7736 |
Reflection shell | Resolution: 2→2.07 Å |
Reflection | *PLUS Num. obs: 7790 / % possible obs: 99.4 % / Redundancy: 3.8 % / Num. measured all: 56243 / Rmerge(I) obs: 0.05 |
Reflection shell | *PLUS Highest resolution: 2 Å / % possible obs: 95.5 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.439 / Mean I/σ(I) obs: 2.11 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refinement | *PLUS Lowest resolution: 30 Å / Rfactor obs: 0.235 / Rfactor Rfree: 0.261 / Rfactor Rwork: 0.235 | ||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||
Refine LS restraints | *PLUS
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