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- PDB-6e50: Crystal structure of the apo domain-swapped dimer Q108K:K40L:T51F... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6.0E+50 | ||||||
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Title | Crystal structure of the apo domain-swapped dimer Q108K:K40L:T51F mutant of human Cellular Retinol Binding Protein II | ||||||
![]() | Retinol-binding protein 2 | ||||||
![]() | CYTOSOLIC PROTEIN / Retinol / iLBP / Protein Switch | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | 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 | ![]() | 43.2 KB | Display | ![]() |
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PDB format | ![]() | 28.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 926.8 KB | Display | ![]() |
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Full document | ![]() | 927.7 KB | Display | |
Data in XML | ![]() | 7.6 KB | Display | |
Data in CIF | ![]() | 9.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6e51C ![]() 6e5eC ![]() 6e5qC ![]() 6e5rC ![]() 6e5sC ![]() 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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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 15628.552 Da / Num. of mol.: 1 / Mutation: Q108K, K40L, T51F Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: Bacterial expression vector pBEN1-SGC (others) References: UniProt: P50120 | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.49 % |
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Crystal grow | Temperature: 298 K / Method: evaporation / Details: PEG 4000, sodium acetate, Ammonium acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Jun 5, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 1.965→28.12 Å / Num. all: 10581 / Num. obs: 8891 / % possible obs: 84.05 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.057 / Rrim(I) all: 0.067 / Net I/σ(I): 23.78 |
Reflection shell | Resolution: 1.965→2.036 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.43 / Num. unique obs: 879 / Rrim(I) all: 0.505 / % possible all: 85.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2RCQ Resolution: 1.965→28.12 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.17
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.965→28.12 Å
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Refine LS restraints |
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LS refinement shell |
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