+Open data
-Basic information
Entry | Database: PDB / ID: 4f3d | ||||||
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Title | Structure of RPE65: P65 crystal form grown in Fos-Choline-10 | ||||||
Components | Retinoid isomerohydrolase | ||||||
Keywords | ISOMERASE / HYDROLASE / monotopic membrane protein / metalloprotein / non-heme iron protein / Beta-propeller / smooth ER membrane | ||||||
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 / phosphatidylcholine 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 / 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 / FOURIER SYNTHESIS / Resolution: 2.5 Å | ||||||
Authors | Kiser, P.D. / Palczewski, K. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2012 Title: Structure of RPE65 isomerase in a lipidic matrix reveals roles for phospholipids and iron in catalysis. Authors: Kiser, P.D. / Farquhar, E.R. / Shi, W. / Sui, X. / Chance, M.R. / Palczewski, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4f3d.cif.gz | 215.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4f3d.ent.gz | 172.9 KB | Display | PDB format |
PDBx/mmJSON format | 4f3d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4f3d_validation.pdf.gz | 444.3 KB | Display | wwPDB validaton report |
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Full document | 4f3d_full_validation.pdf.gz | 447.7 KB | Display | |
Data in XML | 4f3d_validation.xml.gz | 35.5 KB | Display | |
Data in CIF | 4f3d_validation.cif.gz | 49.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f3/4f3d ftp://data.pdbj.org/pub/pdb/validation_reports/f3/4f3d | HTTPS FTP |
-Related structure data
Related structure data | 4f2zC 4f30C 4f3aC 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) / Tissue: retina / Tissue fraction: RPE microsomes / References: UniProt: Q28175, retinoid isomerohydrolase #2: Chemical | #3: Chemical | #4: 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: 3.14 Å3/Da / Density % sol: 60.82 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 35% 2-ethoxyethanol, 22 mM Fos-choline-10, pH 6.5, 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: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 12, 2012 |
Radiation | Monochromator: Kohzu HLD8-24 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 52159 / Num. obs: 52159 / % possible obs: 99.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 49.7 Å2 / Rmerge(I) obs: 0.113 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 2.5→2.65 Å / Redundancy: 3.75 % / Rmerge(I) obs: 0.882 / Mean I/σ(I) obs: 1.53 / Num. unique all: 8474 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 3FSN Resolution: 2.5→47.8 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.935 / SU B: 5.116 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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: 45.362 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→47.8 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 32589 / Refine-ID: X-RAY DIFFRACTION / Rms: 0.04 / Type: interatomic distance / Weight: 0.05
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LS refinement shell | Resolution: 2.5→2.565 Å / Total num. of bins used: 20
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