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Yorodumi- PDB-5u9a: Crystal structure of the FKBP domain of human aryl hydrocarbon re... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5u9a | ||||||
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Title | Crystal structure of the FKBP domain of human aryl hydrocarbon receptor-interacting protein-like 1 (AIPL1) | ||||||
Components | Aryl hydrocarbon receptor-interacting protein-like 1 (AIPL1) | ||||||
Keywords | SIGNALING PROTEIN / AIPL1 / FKBP / chaperone / PDE6 / photoreceptor / LCA / isoprenyl | ||||||
Function / homology | Function and homology information 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 / negative regulation of apoptotic process / apoptotic process / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Yadav, R.P. / Gakhar, L. / Liping, Y. / Artemyev, N.O. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5u9a.cif.gz | 45.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5u9a.ent.gz | 30.5 KB | Display | PDB format |
PDBx/mmJSON format | 5u9a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5u9a_validation.pdf.gz | 428.7 KB | Display | wwPDB validaton report |
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Full document | 5u9a_full_validation.pdf.gz | 429.7 KB | Display | |
Data in XML | 5u9a_validation.xml.gz | 7.6 KB | Display | |
Data in CIF | 5u9a_validation.cif.gz | 9.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u9/5u9a ftp://data.pdbj.org/pub/pdb/validation_reports/u9/5u9a | HTTPS FTP |
-Related structure data
Related structure data | 5u9iC 5u9jC 5u9kC 5v35C 4lavS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 19327.109 Da / Num. of mol.: 1 / Fragment: UNP residues 2-161 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AIPL1, AIPL2 / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q9NZN9 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.13 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop 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: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å |
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Sep 22, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→53.52 Å / Num. obs: 5331 / % possible obs: 100 % / Redundancy: 13.8 % / Biso Wilson estimate: 56.92 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.077 / Net I/σ(I): 24.9 |
Reflection shell | Resolution: 2.7→2.85 Å / Redundancy: 13 % / Rmerge(I) obs: 0.692 / Mean I/σ(I) obs: 4.4 / Num. unique obs: 764 / CC1/2: 0.982 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4LAV Resolution: 2.7→53.52 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.911 / SU B: 21.702 / SU ML: 0.405 / Cross valid method: THROUGHOUT / ESU R: 1.983 / ESU R Free: 0.394 / 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: 76.114 Å2
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Refinement step | Cycle: 1 / Resolution: 2.7→53.52 Å
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Refine LS restraints |
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