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- PDB-5v35: Crystal structure of V71F mutant of the FKBP domain of human aryl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5v35 | ||||||
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Title | Crystal structure of V71F mutant of the FKBP domain of human aryl hydrocarbon receptor-interacting protein-like 1 (AIPL1) complexed with S-farnesyl-L-cysteine methyl ester | ||||||
![]() | Aryl hydrocarbon receptor-interacting protein-like 1 (AIPL1) | ||||||
![]() | SIGNALING PROTEIN / AIPL1 / FKBP / chaperone / PDE6 / photoreceptor / LCA / isoprenyl | ||||||
Function / homology | ![]() farnesylated protein binding / regulation of opsin-mediated signaling pathway / protein farnesylation / phototransduction, visible light / retina homeostasis / visual perception / photoreceptor inner segment / peptidyl-prolyl cis-trans isomerase activity / unfolded protein binding / nuclear speck ...farnesylated protein binding / regulation of opsin-mediated signaling pathway / protein farnesylation / phototransduction, visible light / retina homeostasis / visual perception / photoreceptor inner segment / peptidyl-prolyl cis-trans isomerase activity / unfolded protein binding / nuclear speck / apoptotic process / negative regulation of apoptotic process / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yadav, R.P. / Gakhar, L. / Liping, Y. / Artemyev, N.O. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Unique structural features of the AIPL1-FKBP domain that support prenyl lipid binding and underlie protein malfunction in blindness. Authors: Yadav, R.P. / Gakhar, L. / Yu, L. / Artemyev, N.O. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 45.6 KB | Display | ![]() |
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PDB format | ![]() | 29.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 439 KB | Display | ![]() |
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Full document | ![]() | 440.1 KB | Display | |
Data in XML | ![]() | 8 KB | Display | |
Data in CIF | ![]() | 9.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5u9aSC ![]() 5u9iC ![]() 5u9jC ![]() 5u9kC 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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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 19375.152 Da / Num. of mol.: 1 / Fragment: UNP residues 2-161 / Mutation: V71F Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-FAR / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.81 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion Details: 100 mM Na-Citrate 20 % (W/V) PEG 4000 20 % (V/V) 2-Propanol PH range: 5-7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Nov 9, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→53.475 Å / Num. obs: 6744 / % possible obs: 99.8 % / Redundancy: 13.8 % / Biso Wilson estimate: 63.99 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Net I/σ(I): 23.8 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 13 % / Rmerge(I) obs: 0.681 / Mean I/σ(I) obs: 3.5 / Num. unique all: 741 / CC1/2: 0.984 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5U9A Resolution: 2.5→53.47 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.938 / SU B: 14.423 / SU ML: 0.292 / Cross valid method: THROUGHOUT / ESU R: 0.468 / ESU R Free: 0.299 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 76.432 Å2
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Refinement step | Cycle: 1 / Resolution: 2.5→53.47 Å
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Refine LS restraints |
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