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- PDB-6mkv: Crystal structure of Retinal-bound holo Q108K:K40L:T51W domain-sw... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6mkv | ||||||
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Title | Crystal structure of Retinal-bound holo Q108K:K40L:T51W domain-swapped dimer of human cellular retinol binding protein 2 | ||||||
![]() | Retinol-binding protein 2 | ||||||
![]() | LIPID BINDING PROTEIN / iLBP / Protein Switch / ![]() | ||||||
Function / homology | ![]() vitamin A metabolic process / ![]() ![]() ![]() ![]() ![]() ![]() 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 | ![]() | 125.9 KB | Display | ![]() |
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PDB format | ![]() | 97.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6e50C ![]() 6e51C ![]() 6e5eC ![]() 6e5qC ![]() 6e5rC ![]() 6e5sC ![]() 6e6lC ![]() 6e7mC ![]() 6mcuC ![]() 6mcvC ![]() 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 15667.587 Da / Num. of mol.: 4 / Mutation: Q108K,K40L,T51W Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: Bacterial expression vector pBEN1-SGC (others) References: UniProt: P50120 #2: Chemical | ![]() #3: Chemical | ChemComp-ACT / ![]() #4: Chemical | ![]() #5: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.8 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 4000, Sodium acetate, Ammonium acetate / PH range: 4-4.8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Mar 18, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.107→39.17 Å / Num. obs: 29781 / % possible obs: 96.5 % / Redundancy: 3 % / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.06 / Rrim(I) all: 0.109 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 2.107→2.14 Å / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2740 / Rrim(I) all: 0.66 / % possible all: 91.4 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 2RCQ Resolution: 2.107→39.167 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.78
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.107→39.167 Å
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Refine LS restraints |
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LS refinement shell |
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