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- PDB-4efg: Crystal Structure of the Q108K:K40L:T51V:T53C:Y19W:R58W:T29L Muta... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4efg | ||||||
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Title | Crystal Structure of the Q108K:K40L:T51V:T53C:Y19W:R58W:T29L Mutant of Cellular Retinol Binding Protein Type II in Complex with All-trans-Retinal at 1.58 Angstrom Resolution | ||||||
![]() | 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 | ![]() | 74.8 KB | Display | ![]() |
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PDB format | ![]() | 54.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4edeC ![]() 4eejC ![]() 4exzC ![]() 4gkcC ![]() 4ruuC ![]() 2rcqS C: citing same article ( S: Starting model for refinement |
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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: 15646.653 Da / Num. of mol.: 2 / Mutation: Q108K:K40L:T51V:T53C:Y19W:R58W:T29L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.69 % |
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Crystal grow | Temperature: 298 K / Method: evaporation, recrystallization / pH: 4.6 Details: 40% PEG4000, 0.1 M sodium acetate trihydrate, pH 4.6, 0.1 M ammonium acetate, EVAPORATION, RECRYSTALLIZATION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Details: mirror |
Radiation | Monochromator: Kohzu Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1272 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→28.91 Å / Num. all: 33876 / Num. obs: 33875 |
Reflection shell | Highest resolution: 1.58 Å |
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Processing
Software |
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Refinement | Method to determine structure: MOLREP Starting model: PDB ENTRY 2RCQ Resolution: 1.58→28.91 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.083 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: 23.807 Å2
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Refinement step | Cycle: LAST / Resolution: 1.58→28.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.58→1.621 Å / Total num. of bins used: 20
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