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Open data
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Basic information
Entry | Database: PDB / ID: 6s8x | ||||||
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Title | Crystal structure of the Rab-binding domain of FIP2 | ||||||
![]() | Rab11 family-interacting protein 2 | ||||||
![]() | SIGNALING PROTEIN / membrane trafficking / Rab small GTPases / effector protein / Rab-binding domain / endosomal trafficking | ||||||
Function / homology | ![]() TRAM-dependent toll-like receptor 4 signaling pathway / regulated exocytosis / insulin secretion involved in cellular response to glucose stimulus / establishment of cell polarity / phagocytic cup / phagocytosis / positive regulation of GTPase activity / cell projection / positive regulation of protein localization to plasma membrane / cytoplasmic vesicle membrane ...TRAM-dependent toll-like receptor 4 signaling pathway / regulated exocytosis / insulin secretion involved in cellular response to glucose stimulus / establishment of cell polarity / phagocytic cup / phagocytosis / positive regulation of GTPase activity / cell projection / positive regulation of protein localization to plasma membrane / cytoplasmic vesicle membrane / small GTPase binding / Vasopressin regulates renal water homeostasis via Aquaporins / recycling endosome membrane / endosome / intracellular membrane-bounded organelle / protein kinase binding / protein homodimerization activity / nucleoplasm / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Kearney, A.M. / Khan, A.R. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of the Rab-binding domain of Rab11 family-interacting protein 2. Authors: Kearney, A.M. / Khan, A.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 163.7 KB | Display | ![]() |
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PDB format | ![]() | 110.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 454.5 KB | Display | ![]() |
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Full document | ![]() | 456.2 KB | Display | |
Data in XML | ![]() | 10 KB | Display | |
Data in CIF | ![]() | 13 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 9121.314 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-HEZ / | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.75 Å3/Da / Density % sol: 67.17 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop Details: 0.01M cobat chloride 0.1M NaOAc, pH 4.7 1M 1,6 hexanediol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 12, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.29→46.16 Å / Num. all: 72768 / Num. obs: 16934 / % possible obs: 99.4 % / Redundancy: 4.3 % / Biso Wilson estimate: 35.97 Å2 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.059 / Rrim(I) all: 0.126 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 2.29→2.37 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.872 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1611 / CC1/2: 0.712 / Rpim(I) all: 0.483 / Rrim(I) all: 1.048 / % possible all: 99.3 |
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Processing
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Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 2.29→43.02 Å / SU ML: 0.2621 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.3366
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.36 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.29→43.02 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 24.7894067103 Å / Origin y: 38.4361092945 Å / Origin z: 66.7265682416 Å
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Refinement TLS group | Selection details: all |