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Open data
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Basic information
Entry | Database: PDB / ID: 1z07 | ||||||
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Title | GppNHp-Bound Rab5c G55Q mutant GTPase | ||||||
![]() | Ras-related protein Rab-5C | ||||||
![]() | PROTEIN TRANSPORT / Rab GTPase / Rab5 / Vesicular trafficking | ||||||
Function / homology | ![]() RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / Golgi Associated Vesicle Biogenesis / endosome organization / Clathrin-mediated endocytosis / regulation of endocytosis / endocytic vesicle / endomembrane system / Neutrophil degranulation / small monomeric GTPase ...RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / Golgi Associated Vesicle Biogenesis / endosome organization / Clathrin-mediated endocytosis / regulation of endocytosis / endocytic vesicle / endomembrane system / Neutrophil degranulation / small monomeric GTPase / G protein activity / intracellular protein transport / synaptic vesicle membrane / endocytosis / GDP binding / melanosome / early endosome membrane / GTPase activity / GTP binding / Golgi apparatus / plasma membrane 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 | ![]() | 53.9 KB | Display | ![]() |
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PDB format | ![]() | 36.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 728.5 KB | Display | ![]() |
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Full document | ![]() | 729.2 KB | Display | |
Data in XML | ![]() | 11.3 KB | Display | |
Data in CIF | ![]() | 16.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1yu9C ![]() 1yvdC ![]() 1yzkC ![]() 1yzlC ![]() 1yzmC ![]() 1yznC ![]() 1yzqC ![]() 1yztC ![]() 1yzuC ![]() 1z06C ![]() 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: 18489.035 Da / Num. of mol.: 1 / Fragment: GTPase domain / Mutation: G55Q 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: 2.11 Å3/Da / Density % sol: 41.14 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 10% PEG 6000, 50mM MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-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: Jan 2, 2004 / 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: 1.8→50 Å / Num. obs: 12697 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 23.1 Å2 / Rsym value: 0.058 / Net I/σ(I): 16 |
Reflection shell | Resolution: 1.8→1.85 Å / Redundancy: 3 % / Mean I/σ(I) obs: 5 / Num. unique all: 880 / Rsym value: 0.229 / % possible all: 73.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: Polyalanine Rab5c GTPase Resolution: 1.81→8 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.926 / SU B: 2.474 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.15 / ESU R Free: 0.152 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.35 Å2
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Refinement step | Cycle: LAST / Resolution: 1.81→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.808→1.853 Å / Total num. of bins used: 20
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