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- PDB-6c7p: Crystal structure of D477G ACO/RPE65 chimera, monoclinic crystal form -
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Open data
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Basic information
Entry | Database: PDB / ID: 6c7p | |||||||||
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Title | Crystal structure of D477G ACO/RPE65 chimera, monoclinic crystal form | |||||||||
![]() | Apocarotenoid-15,15'-oxygenase | |||||||||
![]() | OXIDOREDUCTASE / non-heme iron / chimera / 7-bladed propeller / dominant mutation | |||||||||
Function / homology | ![]() all-trans-8'-apo-beta-carotenal 15,15'-oxygenase / all-trans-8'-apo-beta-carotenal 15,15'-oxygenase activity / carotenoid dioxygenase activity / 9-cis-epoxycarotenoid dioxygenase activity / carotene catabolic process / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Kiser, P.D. / Shi, W. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Insights into the pathogenesis of dominant retinitis pigmentosa associated with a D477G mutation in RPE65. Authors: Choi, E.H. / Suh, S. / Sander, C.L. / Hernandez, C.J.O. / Bulman, E.R. / Khadka, N. / Dong, Z. / Shi, W. / Palczewski, K. / Kiser, P.D. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 197.6 KB | Display | ![]() |
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PDB format | ![]() | 156 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 432.7 KB | Display | ![]() |
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Full document | ![]() | 435.9 KB | Display | |
Data in XML | ![]() | 32.6 KB | Display | |
Data in CIF | ![]() | 44.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6c7kSC ![]() 6c7oC 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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2 | ![]()
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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: THR / End label comp-ID: THR / Refine code: _ / Auth seq-ID: 11 - 490 / Label seq-ID: 11 - 490
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Components
#1: Protein | Mass: 54401.344 Da / Num. of mol.: 2 Mutation: P44L, D45W, P431S, R432H, G434D, G435A, V436L, A437E, W442V, D461N, Q463K Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: PCC 6803 / Kazusa / Gene: sll1541 / Production host: ![]() ![]() References: UniProt: P74334, all-trans-8'-apo-beta-carotenal 15,15'-oxygenase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.6 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1 M Bis-Tris propane, pH 6 and 21% w/v sodium polyacrylate 2100 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 22, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918401 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 31744 / % possible obs: 96.7 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 2.6→2.76 Å / Redundancy: 3 % / Rmerge(I) obs: 0.998 / Mean I/σ(I) obs: 0.93 / Num. unique obs: 5023 / % possible all: 96 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6C7K Resolution: 2.6→41.76 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.937 / SU B: 19.865 / SU ML: 0.36 / Cross valid method: THROUGHOUT / ESU R Free: 0.347 / 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 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 77.163 Å2
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Refinement step | Cycle: 1 / Resolution: 2.6→41.76 Å
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Refine LS restraints |
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