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Open data
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Basic information
Entry | Database: PDB / ID: 3cpj | ||||||
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Title | Crystal structure of Ypt31 in complex with yeast Rab-GDI | ||||||
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![]() | PROTEIN TRANSPORT / Rab GTPase / prenylation / vesicular transport / Acetylation / Golgi apparatus / GTP-binding / Lipoprotein / Membrane / Nucleotide-binding / Cytoplasm / GTPase activation / Phosphoprotein | ||||||
Function / homology | ![]() Rab GDP-dissociation inhibitor activity / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / early endosome to Golgi transport / small GTPase-mediated signal transduction / exocytosis / vesicle-mediated transport / Neutrophil degranulation / GTPase activator activity / trans-Golgi network ...Rab GDP-dissociation inhibitor activity / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / early endosome to Golgi transport / small GTPase-mediated signal transduction / exocytosis / vesicle-mediated transport / Neutrophil degranulation / GTPase activator activity / trans-Golgi network / recycling endosome / autophagy / protein transport / mitochondrial outer membrane / endosome / Golgi membrane / GTPase activity / GTP binding / Golgi apparatus / mitochondrion / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kravchenko, S. / Ignatev, A. / Goody, R.S. / Rak, A. / Pylypenko, O. | ||||||
![]() | ![]() Title: A structural model of the GDP dissociation inhibitor rab membrane extraction mechanism. Authors: Ignatev, A. / Kravchenko, S. / Rak, A. / Goody, R.S. / Pylypenko, O. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 144.7 KB | Display | ![]() |
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PDB format | ![]() | 109.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 791.6 KB | Display | ![]() |
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Full document | ![]() | 801.3 KB | Display | |
Data in XML | ![]() | 27.9 KB | Display | |
Data in CIF | ![]() | 41.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3cphC ![]() 3cpiC ![]() 1ukvS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 2 types, 2 molecules GB
#1: Protein | Mass: 51271.230 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Plasmid: pET19 / Species (production host): Escherichia coli / Production host: ![]() ![]() |
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#2: Protein | Mass: 24508.014 Da / Num. of mol.: 1 / Mutation: D58E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Plasmid: pET19 / Species (production host): Escherichia coli / Production host: ![]() ![]() |
-Non-polymers , 4 types, 456 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-MG / | #5: Chemical | ChemComp-GDP / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.93 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 20% PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→19.79 Å / Num. all: 30772 / Num. obs: 30683 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 2.35→2.4 Å / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1ukv, chain G Resolution: 2.35→19.79 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.889 / SU B: 7.523 / SU ML: 0.183 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.389 / ESU R Free: 0.26 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 42.168 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.35→19.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.35→2.41 Å / Total num. of bins used: 20
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