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- PDB-6e5s: Crystal structure of holo retinal-bound domain-swapped dimer Q108... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6e5s | ||||||
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Title | Crystal structure of holo retinal-bound domain-swapped dimer Q108K:T51D mutant of human Cellular Retinol Binding Protein II | ||||||
![]() | Retinol-binding protein 2 | ||||||
![]() | LIPID BINDING PROTEIN / Retinol / iLBP / Protein Switch / CYTOSOLIC PROTEIN | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Nosrati, M. / Ghanbarpour, A. / Geiger, J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Engineering the hCRBPII Domain-Swapped Dimer into a New Class of Protein Switches. Authors: Ghanbarpour, A. / Pinger, C. / Esmatpour Salmani, R. / Assar, Z. / Santos, E.M. / Nosrati, M. / Pawlowski, K. / Spence, D. / Vasileiou, C. / Jin, X. / 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 | ![]() | 345.9 KB | Display | ![]() |
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PDB format | ![]() | 283.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 65 KB | Display | |
Data in CIF | ![]() | 87.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6e50C ![]() 6e51C ![]() 6e5eC ![]() 6e5qC ![]() 6e5rC ![]() 6e6lC ![]() 6e7mC ![]() 6mcuC ![]() 6mcvC ![]() 6mkvC ![]() 6mlbC ![]() 6on5C ![]() 6on7C ![]() 6on8C ![]() 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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Unit cell |
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Components
#1: Protein | Mass: 15612.487 Da / Num. of mol.: 12 / Mutation: Q108K, T51D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: Bacterial expression vector pBEN1-SGC (others) References: UniProt: P50120 #2: Chemical | ChemComp-RET / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.61 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG 4000, sodium acetate, Ammonium acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Aug 17, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0782 Å / Relative weight: 1 |
Reflection | Resolution: 2.061→45.46 Å / Num. obs: 108095 / % possible obs: 91.86 % / Redundancy: 5 % / Biso Wilson estimate: 35.24 Å2 / Rrim(I) all: 0.083 / Net I/σ(I): 22 |
Reflection shell | Resolution: 2.061→2.13 Å / Rrim(I) all: 0.939 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2RCQ Resolution: 2.061→45.459 Å / SU ML: 0.71 / Cross valid method: FREE R-VALUE / σ(F): 0.16 / Phase error: 29.14
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Bsol: 41.723 Å2 / ksol: 0.343 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.061→45.459 Å
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Refine LS restraints |
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LS refinement shell |
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