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- PDB-7k3i: Cellular retinol-binding protein 2 (CRBP2) in complex with 2-laur... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7k3i | |||||||||
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Title | Cellular retinol-binding protein 2 (CRBP2) in complex with 2-lauroylglycerol | |||||||||
![]() | Retinol-binding protein 2 | |||||||||
![]() | LIPID BINDING PROTEIN / lauroylglycerol / monoacylglycerol / retinol-binding protein / lipid binding | |||||||||
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 | ![]() ![]() ![]() | |||||||||
![]() | Adams, C. / Silvaroli, J.A. / Banarjee, S. / Golczak, M. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Molecular basis for the interaction of cellular retinol binding protein 2 (CRBP2) with nonretinoid ligands. Authors: Silvaroli, J.A. / Plau, J. / Adams, C.H. / Banerjee, S. / Widjaja-Adhi, M.A.K. / Blaner, W.S. / Golczak, M. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 118.6 KB | Display | ![]() |
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PDB format | ![]() | 91.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 651.7 KB | Display | ![]() |
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Full document | ![]() | 651.7 KB | Display | |
Data in XML | ![]() | 12.3 KB | Display | |
Data in CIF | ![]() | 19.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7jvgSC ![]() 7jvyC ![]() 7jwdC ![]() 7jwrC ![]() 7jx2C ![]() 7jz5C 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: 16195.246 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-VLZ / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.59 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: Tris/HCl Ph 8.0, PEG3350 20%-25% |
-Data collection
Diffraction | Mean temperature: 90 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 18, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→64.56 Å / Num. obs: 51014 / % possible obs: 98.8 % / Redundancy: 6.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.045 / Rrim(I) all: 0.085 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 1.2→1.22 Å / Rmerge(I) obs: 0.899 / Num. unique obs: 2139 / CC1/2: 0.671 / Rpim(I) all: 0.664 / % possible all: 85.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7JVG Resolution: 1.2→46.499 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.45 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→46.499 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 4.6575 Å / Origin y: 10.8772 Å / Origin z: 15.8687 Å
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Refinement TLS group | Selection details: all |