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Open data
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Basic information
Entry | Database: PDB / ID: 1yzq | ||||||
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Title | GppNHp-Bound Rab6 GTPase | ||||||
![]() | small GTP binding protein RAB6 isoform | ||||||
![]() | PROTEIN TRANSPORT / Rab GTPase / Rab6 / Vesicular trafficking | ||||||
Function / homology | ![]() peptidyl-cysteine methylation / minus-end-directed organelle transport along microtubule / protein localization to Golgi membrane / endosome to plasma membrane transport vesicle / early endosome to Golgi transport / Retrograde transport at the Trans-Golgi-Network / acrosomal membrane / protein localization to Golgi apparatus / Pre-NOTCH Processing in Golgi / RAB geranylgeranylation ...peptidyl-cysteine methylation / minus-end-directed organelle transport along microtubule / protein localization to Golgi membrane / endosome to plasma membrane transport vesicle / early endosome to Golgi transport / Retrograde transport at the Trans-Golgi-Network / acrosomal membrane / protein localization to Golgi apparatus / Pre-NOTCH Processing in Golgi / RAB geranylgeranylation / myosin V binding / intra-Golgi vesicle-mediated transport / COPI-independent Golgi-to-ER retrograde traffic / RAB GEFs exchange GTP for GDP on RABs / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / retrograde transport, endosome to Golgi / TBC/RABGAPs / antigen processing and presentation / localization / endomembrane system / secretory granule membrane / trans-Golgi network membrane / intracellular protein transport / trans-Golgi network / neuron projection development / cytoplasmic vesicle / protein domain specific binding / Golgi membrane / GTPase activity / Neutrophil degranulation / endoplasmic reticulum membrane / GTP binding / Golgi apparatus / extracellular exosome / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Eathiraj, S. / Pan, X. / Ritacco, C. / Lambright, D.G. | ||||||
![]() | ![]() Title: Structural basis of family-wide Rab GTPase recognition by rabenosyn-5. Authors: Eathiraj, S. / Pan, X. / Ritacco, C. / Lambright, D.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 51.7 KB | Display | ![]() |
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PDB format | ![]() | 35.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 776.1 KB | Display | ![]() |
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Full document | ![]() | 779 KB | Display | |
Data in XML | ![]() | 11.2 KB | Display | |
Data in CIF | ![]() | 15.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1yu9C ![]() 1yvdC ![]() 1yzkC ![]() 1yzlC ![]() 1yzmC ![]() 1yznC ![]() 1yztC ![]() 1yzuC ![]() 1z06C ![]() 1z07C ![]() 1z08C ![]() 1z0aC ![]() 1z0dC ![]() 1z0fC ![]() 1z0iC ![]() 1z0jC ![]() 1z0kC ![]() 1z22C ![]() 1z2aC C: citing same article ( |
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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
#1: Protein | Mass: 19372.139 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-GNP / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 54.92 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 20% PEG 6000, 300mM Magnesium Chloride, 10% glycerol, 50mM HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 278K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: May 13, 2003 / Details: Osmic mirror |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→50 Å / Num. obs: 20059 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 36 Å2 / Rsym value: 0.058 / Net I/σ(I): 27.7 |
Reflection shell | Resolution: 1.78→1.83 Å / Redundancy: 5 % / Mean I/σ(I) obs: 6.2 / Num. unique all: 1576 / Rsym value: 0.282 / % possible all: 95.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: Polyalanine Rab3a GTPase Resolution: 1.78→6 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.931 / SU B: 2.861 / SU ML: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.146 / ESU R Free: 0.138 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.115 Å2
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Refinement step | Cycle: LAST / Resolution: 1.78→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.78→1.822 Å / Total num. of bins used: 20
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