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Open data
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Basic information
Entry | Database: PDB / ID: 1yzm | ||||||
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Title | Structure of Rabenosyn (458-503), Rab4 binding domain | ||||||
![]() | FYVE-finger-containing Rab5 effector protein rabenosyn-5 | ||||||
![]() | PROTEIN TRANSPORT / Rab Effector / Rabenosyn / Rab GTPase / vesicular trafficking | ||||||
Function / homology | ![]() regulation of Golgi organization / Toll Like Receptor 9 (TLR9) Cascade / Golgi to lysosome transport / early endosome to Golgi transport / endosomal transport / small GTPase binding / protein transport / Factors involved in megakaryocyte development and platelet production / early endosome membrane / endosome membrane ...regulation of Golgi organization / Toll Like Receptor 9 (TLR9) Cascade / Golgi to lysosome transport / early endosome to Golgi transport / endosomal transport / small GTPase binding / protein transport / Factors involved in megakaryocyte development and platelet production / early endosome membrane / endosome membrane / endosome / intracellular membrane-bounded organelle / zinc ion binding / extracellular exosome / 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 | ![]() | 22.8 KB | Display | ![]() |
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PDB format | ![]() | 13.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 412.9 KB | Display | ![]() |
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Full document | ![]() | 413 KB | Display | |
Data in XML | ![]() | 4.6 KB | Display | |
Data in CIF | ![]() | 6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1yu9C ![]() 1yvdC ![]() 1yzkC ![]() 1yzlC ![]() 1yznC ![]() 1yzqC ![]() 1yztC ![]() 1yzuC ![]() 1z06C ![]() 1z07C ![]() 1z08C ![]() 1z0aC ![]() 1z0dC ![]() 1z0fC ![]() 1z0iC ![]() 1z0jC ![]() 1z0kC ![]() 1z22C ![]() 1z2aC ![]() 1aikS S: Starting model for refinement 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: 5901.560 Da / Num. of mol.: 1 Fragment: RAB4 binding domain, sequence database residues 458-503 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 47.74 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 10% PEG 6000, 50mM Na acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 4K |
-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: Nov 3, 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: 1.5→50 Å / Num. obs: 7561 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 25 Å2 / Rsym value: 0.07 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 1.5→1.54 Å / Redundancy: 3 % / Mean I/σ(I) obs: 5.8 / Num. unique all: 531 / Rsym value: 0.221 / % possible all: 80.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: Polyalanine-gp41 (PDB ID; 1AIK.pdb) Resolution: 1.5→6 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.375 / SU ML: 0.052 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.084 / ESU R Free: 0.08 / 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: 14.817 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.502→1.539 Å / Total num. of bins used: 20
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