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- PDB-4gkc: Crystal structure of Q108K:K40L:T51V:T53C:R58W:T29L:Y19W:Q4A muta... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4gkc | ||||||
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Title | Crystal structure of Q108K:K40L:T51V:T53C:R58W:T29L:Y19W:Q4A mutant of cellular retinol binding protein II complex with all-trans-retinal at 1.33 | ||||||
![]() | Retinol-binding protein 2 | ||||||
![]() | TRANSPORT PROTEIN / Retinal complex+ beta barrel | ||||||
Function / homology | ![]() vitamin A metabolic process / retinoid binding / retinal binding / retinol binding / epidermis development / fatty acid transport / Retinoid metabolism and transport / fatty acid binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nossoni, Z. / Geiger, J.H. | ||||||
![]() | ![]() Title: Tuning the electronic absorption of protein-embedded all-trans-retinal. Authors: Wang, W. / Nossoni, Z. / Berbasova, T. / Watson, C.T. / Yapici, I. / Lee, K.S. / Vasileiou, C. / Geiger, J.H. / Borhan, B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 78.5 KB | Display | ![]() |
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PDB format | ![]() | 58.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 807.7 KB | Display | ![]() |
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Full document | ![]() | 816.8 KB | Display | |
Data in XML | ![]() | 18.5 KB | Display | |
Data in CIF | ![]() | 26.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4edeC ![]() 4eejC ![]() 4efgC ![]() 4exzC ![]() 4ruuC ![]() 2rcqS 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: 15589.603 Da / Num. of mol.: 2 / Mutation: Q108K,K40L,T51V,T53C,Y19W,R58W,T29L,Q4A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.69 % |
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Crystal grow | Temperature: 298 K / Method: evaporation / pH: 4.6 Details: 40% PEG 4000, 0.1M CH3COONa.3H2O, 0.1 M CH3COONH4, EVAPORATION, temperature 298K, pH 4.6 |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR300 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1272 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→28.122 Å / Num. all: 179578 / Num. obs: 50433 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2rcq Resolution: 1.3→28.12 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.939 / SU B: 0.831 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.071 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.607 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→28.12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.301→1.334 Å / Total num. of bins used: 20
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