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Yorodumi- PDB-4ryx: Crystal structure of RPE65 in complex with emixustat and palmitat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ryx | ||||||
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Title | Crystal structure of RPE65 in complex with emixustat and palmitate, P6522 crystal form | ||||||
Components | Retinoid isomerohydrolase | ||||||
Keywords | ISOMERASE / 7-bladed beta propeller / monotopic membrane protein / non-heme iron enzyme / retinoid isomerase / HYDROLASE | ||||||
Function / homology | Function and homology information retinoid isomerohydrolase / lutein isomerase / retinol isomerase activity / all-trans-retinyl-palmitate hydrolase, 11-cis retinol forming activity / all-trans-retinyl-ester hydrolase, 11-cis retinol forming activity / zeaxanthin biosynthetic process / beta-carotene 15,15'-dioxygenase activity / The canonical retinoid cycle in rods (twilight vision) / retinal metabolic process / cardiolipin binding ...retinoid isomerohydrolase / lutein isomerase / retinol isomerase activity / all-trans-retinyl-palmitate hydrolase, 11-cis retinol forming activity / all-trans-retinyl-ester hydrolase, 11-cis retinol forming activity / zeaxanthin biosynthetic process / beta-carotene 15,15'-dioxygenase activity / The canonical retinoid cycle in rods (twilight vision) / retinal metabolic process / cardiolipin binding / phosphatidylcholine binding / response to stimulus / phosphatidylserine binding / visual perception / endoplasmic reticulum membrane / identical protein binding / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / rigid body refinement / Resolution: 2 Å | ||||||
Authors | Kiser, P.D. / Palczewski, K. | ||||||
Citation | Journal: J.Clin.Invest. / Year: 2015 Title: Molecular pharmacodynamics of emixustat in protection against retinal degeneration. Authors: Zhang, J. / Kiser, P.D. / Badiee, M. / Palczewska, G. / Dong, Z. / Golczak, M. / Tochtrop, G.P. / Palczewski, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ryx.cif.gz | 130.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ryx.ent.gz | 98.5 KB | Display | PDB format |
PDBx/mmJSON format | 4ryx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ryx_validation.pdf.gz | 955.9 KB | Display | wwPDB validaton report |
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Full document | 4ryx_full_validation.pdf.gz | 959.6 KB | Display | |
Data in XML | 4ryx_validation.xml.gz | 24.4 KB | Display | |
Data in CIF | 4ryx_validation.cif.gz | 36.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ry/4ryx ftp://data.pdbj.org/pub/pdb/validation_reports/ry/4ryx | HTTPS FTP |
-Related structure data
Related structure data | 4ryyC 4ryzC 4zhkC 4f3aS 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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 61040.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q28175, retinoid isomerohydrolase |
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-Non-polymers , 6 types, 398 molecules
#2: Chemical | ChemComp-FE2 / | ||
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#3: Chemical | ChemComp-PLM / | ||
#4: Chemical | ChemComp-A3V / ( | ||
#5: Chemical | ChemComp-SO4 / | ||
#6: Chemical | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.23 Å3/Da / Density % sol: 61.98 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 35% MPD, 200 mM (NH4)2SO4 and 100 mM Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 281K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 24, 2014 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 53112 / Num. obs: 53110 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 2→2.13 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.1231 / Mean I/σ(I) obs: 0.97 / % possible all: 98 |
-Processing
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Refinement | Method to determine structure: rigid body refinement Starting model: 4F3A Resolution: 2→44.15 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.957 / SU B: 4.704 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.771 Å2
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Refinement step | Cycle: LAST / Resolution: 2→44.15 Å
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Refine LS restraints |
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