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- PDB-6mqy: Crystal Structure of the 13-cis Product of All-trans Retinal-Boun... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6mqy | ||||||
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Title | Crystal Structure of the 13-cis Product of All-trans Retinal-Bound R111K:Y134F:T54V:R132Q:P39Y:R59Y:L121E Mutant of Human Cellular Retinoic Acid Binding Protein II Irradiated with 400 nm Laser (30 seconds) at 1.9 Angstrom | ||||||
![]() | Cellular retinoic acid-binding protein 2 | ||||||
![]() | LIPID BINDING PROTEIN / iLBP / Rhodopsin mimic | ||||||
Function / homology | ![]() positive regulation of collateral sprouting / retinoid binding / retinal binding / retinoic acid binding / embryonic forelimb morphogenesis / retinoic acid metabolic process / retinol binding / Signaling by Retinoic Acid / epidermis development / fatty acid transport ...positive regulation of collateral sprouting / retinoid binding / retinal binding / retinoic acid binding / embryonic forelimb morphogenesis / retinoic acid metabolic process / retinol binding / Signaling by Retinoic Acid / epidermis development / fatty acid transport / cyclin binding / fatty acid binding / regulation of DNA-templated transcription / endoplasmic reticulum / signal transduction / extracellular exosome / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ghanbarpour, A. / Geiger, J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Mimicking Microbial Rhodopsin Isomerization in a Single Crystal. Authors: Ghanbarpour, A. / Nairat, M. / Nosrati, M. / Santos, E.M. / Vasileiou, C. / Dantus, M. / Borhan, B. / Geiger, J.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 45.1 KB | Display | ![]() |
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PDB format | ![]() | 29.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 708.3 KB | Display | ![]() |
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Full document | ![]() | 710.1 KB | Display | |
Data in XML | ![]() | 8.3 KB | Display | |
Data in CIF | ![]() | 10.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6mopC ![]() 6moqC ![]() 6morC ![]() 6movC ![]() 6moxC ![]() 6mpkC ![]() 6mqiC ![]() 6mqjC ![]() 6mqwC ![]() 6mqxC ![]() 6mqzC ![]() 6mr0C ![]() 4yfpS 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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Components
#1: Protein | Mass: 15594.747 Da / Num. of mol.: 1 / Mutation: R111K, Y134F, T54V, R132Q, P39Y, R59Y, L121E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: Bacterial expression vector pBEN1-SGC (others) References: UniProt: P29373 | ||||
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#2: Chemical | #3: Chemical | ChemComp-RET / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.15 Å3/Da / Density % sol: 60.91 % / Description: Hexagonal |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG 3350, D-Malic acid |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 21, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97911 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→29.171 Å / Num. obs: 16010 / % possible obs: 99.2 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 35.49 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 1552 / Rrim(I) all: 0.481 / % possible all: 98.66 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4YFP Resolution: 1.9→29.171 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 21.8 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→29.171 Å
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Refine LS restraints |
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LS refinement shell |
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