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Yorodumi- PDB-3tkl: Crystal structure of the GTP-bound Rab1a in complex with the coil... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3tkl | ||||||
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Title | Crystal structure of the GTP-bound Rab1a in complex with the coiled-coil domain of LidA from Legionella pneumophila | ||||||
Components |
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Keywords | PROTEIN TRANSPORT/PROTEIN BINDING / Vesicle trafficking / PROTEIN TRANSPORT-PROTEIN BINDING complex | ||||||
Function / homology | Function and homology information positive regulation of glycoprotein metabolic process / growth hormone secretion / melanosome transport / COPII-coated vesicle cargo loading / vesicle transport along microtubule / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / Golgi Cisternae Pericentriolar Stack Reorganization / COPII-mediated vesicle transport / COPI-dependent Golgi-to-ER retrograde traffic ...positive regulation of glycoprotein metabolic process / growth hormone secretion / melanosome transport / COPII-coated vesicle cargo loading / vesicle transport along microtubule / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / Golgi Cisternae Pericentriolar Stack Reorganization / COPII-mediated vesicle transport / COPI-dependent Golgi-to-ER retrograde traffic / virion assembly / transport vesicle membrane / Golgi organization / autophagosome assembly / endoplasmic reticulum to Golgi vesicle-mediated transport / endomembrane system / COPI-mediated anterograde transport / vesicle-mediated transport / substrate adhesion-dependent cell spreading / small monomeric GTPase / G protein activity / positive regulation of interleukin-8 production / intracellular protein transport / autophagy / endocytosis / melanosome / cell migration / early endosome / defense response to bacterium / cadherin binding / Golgi membrane / GTPase activity / GTP binding / Golgi apparatus / endoplasmic reticulum / extracellular exosome / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Legionella pneumophila (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.183 Å | ||||||
Authors | Cheng, W. / Yin, K. / Lu, D. / Li, B. / Zhu, D. / Chen, Y. / Zhang, H. / Xu, S. / Chai, J. / Gu, L. | ||||||
Citation | Journal: Plos Pathog. / Year: 2012 Title: Structural insights into a unique Legionella pneumophila effector LidA recognizing both GDP and GTP bound Rab1 in their active state Authors: Cheng, W. / Yin, K. / Lu, D. / Li, B. / Zhu, D. / Chen, Y. / Zhang, H. / Xu, S. / Chai, J. / Gu, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3tkl.cif.gz | 92.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3tkl.ent.gz | 66.5 KB | Display | PDB format |
PDBx/mmJSON format | 3tkl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tk/3tkl ftp://data.pdbj.org/pub/pdb/validation_reports/tk/3tkl | HTTPS FTP |
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-Related structure data
Related structure data | 3sfvC 2folS 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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Unit cell |
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-Components
#1: Protein | Mass: 21766.635 Da / Num. of mol.: 1 / Fragment: UNP residues 1-191 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RAB1 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P62820 |
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#2: Protein | Mass: 30634.645 Da / Num. of mol.: 1 / Fragment: Coiled-coil domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila (bacteria) / Strain: Corby / Gene: lidA / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: A5IFX1 |
#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-GTP / |
#5: 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: 1.86 Å3/Da / Density % sol: 33.89 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M HEPES, 25% PEG3350, 0.7% butanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Jun 14, 2010 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.183→50 Å / Num. all: 20017 / Num. obs: 20017 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 25.74 Å2 / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/σ(I): 23.88 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.295 / Mean I/σ(I) obs: 4.65 / Num. unique all: 991 / Rsym value: 0.295 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2FOL Resolution: 2.183→31.785 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.25 / σ(F): 1.35 / σ(I): 0 / Phase error: 25.08 / 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 / Bsol: 37.449 Å2 / ksol: 0.372 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 89.92 Å2 / Biso mean: 32.0164 Å2 / Biso min: 14.28 Å2
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Refinement step | Cycle: LAST / Resolution: 2.183→31.785 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7
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