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- PDB-4jhp: The crystal structure of the RPGR RCC1-like domain in complex wit... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4jhp | ||||||
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Title | The crystal structure of the RPGR RCC1-like domain in complex with PDE6D | ||||||
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![]() | LIPID BINDING PROTEIN / immunoglobulin-like beta-sandwich / RCC1-like domain / beta propellar / seven bladed-propeller / STRUCTURAL PROTEIN | ||||||
Function / homology | ![]() ARL13B-mediated ciliary trafficking of INPP5E / intraciliary transport / GTPase inhibitor activity / response to stimulus / photoreceptor outer segment / cilium assembly / sperm flagellum / visual perception / guanyl-nucleotide exchange factor activity / ciliary basal body ...ARL13B-mediated ciliary trafficking of INPP5E / intraciliary transport / GTPase inhibitor activity / response to stimulus / photoreceptor outer segment / cilium assembly / sperm flagellum / visual perception / guanyl-nucleotide exchange factor activity / ciliary basal body / intracellular protein transport / cytoplasmic vesicle membrane / small GTPase binding / cilium / RAS processing / ubiquitin protein ligase activity / cytoplasmic vesicle / ubiquitin-dependent protein catabolic process / cytoskeleton / protein ubiquitination / centrosome / Golgi apparatus / RNA binding / cytoplasm / cytosol 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 120.7 KB | Display | ![]() |
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PDB format | ![]() | 90.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 432 KB | Display | ![]() |
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Full document | ![]() | 435.9 KB | Display | |
Data in XML | ![]() | 23.2 KB | Display | |
Data in CIF | ![]() | 35 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4jhnSC 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: 17585.121 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 42540.832 Da / Num. of mol.: 1 / Fragment: RPGR (8-368) the RCC1-like domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.14 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.2M sodium chloride, 0.1M HEPES pH 7.5 and 12% (w/v) PEG8000, 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: May 4, 2012 |
Radiation | Monochromator: SAGITALLY - HORIZONTALLY FOCUSED SI(111) MONOCHROMATOR Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97939 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→29.39 Å / Num. all: 47164 / Num. obs: 47164 / % possible obs: 99.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.525 / Mean I/σ(I) obs: 3.43 / % possible all: 99 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4JHN Resolution: 1.9→29.39 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.012 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.133 / 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: 26.379 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→29.39 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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