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Open data
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Basic information
Entry | Database: PDB / ID: 4jhn | ||||||
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Title | The crystal structure of the RPGR RCC1-like domain | ||||||
![]() | X-linked retinitis pigmentosa GTPase regulator | ||||||
![]() | UNKNOWN FUNCTION / RCC1 / beta propellar / seven bladed-propeller | ||||||
Function / homology | ![]() intraciliary transport / photoreceptor outer segment / cilium assembly / sperm flagellum / visual perception / ciliary basal body / guanyl-nucleotide exchange factor activity / intracellular protein transport / ubiquitin protein ligase activity / ubiquitin-dependent protein catabolic process ...intraciliary transport / photoreceptor outer segment / cilium assembly / sperm flagellum / visual perception / ciliary basal body / guanyl-nucleotide exchange factor activity / intracellular protein transport / ubiquitin protein ligase activity / ubiquitin-dependent protein catabolic process / protein ubiquitination / centrosome / Golgi apparatus / RNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Waetzlich, D. / Vetter, I. / Wittinghofer, A. / Ismail, S. | ||||||
![]() | ![]() Title: The interplay between RPGR, PDE-delta and Arl2/3 regulate the ciliary targeting of farnesylated cargo. Authors: Watzlich, D. / Vetter, I. / Gotthardt, K. / Miertzschke, M. / Chen, Y.X. / Wittinghofer, A. / Ismail, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 298 KB | Display | ![]() |
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PDB format | ![]() | 239.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4jhpC ![]() 1a12S 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
#1: Protein | Mass: 45965.641 Da / Num. of mol.: 4 / Fragment: RPGR (1-392) the RCC1-like domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.68 Å3/Da / Density % sol: 26.99 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M LiCl2 and 18% (w/v) PEG3350 and microseeding, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 21, 2010 |
Radiation | Monochromator: SAGITALLY - HORIZONTALLY FOCUSED SI(111) MONOCHROMATOR Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.977 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→29.83 Å / Num. all: 132539 / Num. obs: 132539 / % possible obs: 99.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 1.7→1.8 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 5.17 / % possible all: 99.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1A12 Resolution: 1.7→29.83 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.201 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 21.676 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→29.83 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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