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Yorodumi- PDB-4rsc: Crystal structure of RPE65 in complex with emixustat and palmitate -
+Open data
-Basic information
Entry | Database: PDB / ID: 4rsc | ||||||
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Title | Crystal structure of RPE65 in complex with emixustat and palmitate | ||||||
Components | Retinoid isomerohydrolase | ||||||
Keywords | ISOMERASE / 7-bladed beta propeller / monotopic membrane protein / non-heme iron enzyme / retinoid isomerase / smooth endoplasmic reticulum | ||||||
Function / homology | Function and homology information retinoid isomerohydrolase / lutein isomerase / beta-carotene 15,15'-dioxygenase activity / 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 / The canonical retinoid cycle in rods (twilight vision) / retinal metabolic process / phosphatidylcholine binding ...retinoid isomerohydrolase / lutein isomerase / beta-carotene 15,15'-dioxygenase activity / 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 / The canonical retinoid cycle in rods (twilight vision) / retinal metabolic process / phosphatidylcholine binding / cardiolipin binding / 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 / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Kiser, P.D. / Shi, W. / Palczewski, K. | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2015 Title: Catalytic mechanism of a retinoid isomerase essential for vertebrate vision. Authors: Kiser, P.D. / Zhang, J. / Badiee, M. / Li, Q. / Shi, W. / Sui, X. / 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 | 4rsc.cif.gz | 244 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rsc.ent.gz | 193.4 KB | Display | PDB format |
PDBx/mmJSON format | 4rsc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4rsc_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 4rsc_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 4rsc_validation.xml.gz | 47.3 KB | Display | |
Data in CIF | 4rsc_validation.cif.gz | 71.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rs/4rsc ftp://data.pdbj.org/pub/pdb/validation_reports/rs/4rsc | HTTPS FTP |
-Related structure data
Related structure data | 4rseC 3fsnS S: Starting model for refinement C: citing same article (ref.) |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 3 - 533 / Label seq-ID: 3 - 533
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-Components
#1: Protein | Mass: 61040.195 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q28175, retinoid isomerohydrolase #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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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: 3.17 Å3/Da / Density % sol: 61.14 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 30% PEG200 200 mM ammonium phosphate 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: NSLS / Beamline: X29A / Wavelength: 1.075 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 25, 2014 |
Radiation | Monochromator: Rosenbaum-Rock double crystal sagittal focusing Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 139166 / Num. obs: 139163 / % possible obs: 99.54 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3FSN Resolution: 1.8→47.93 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.923 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.096 / 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: 33.394 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→47.93 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 31861 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.01 Å / Weight position: 0.05
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LS refinement shell | Resolution: 1.805→1.852 Å / Total num. of bins used: 20
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