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Open data
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Basic information
Entry | Database: PDB / ID: 5ljh | ||||||
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Title | Crystal structure of human apo CRBP1/K40L mutant | ||||||
![]() | Retinol-binding protein 1 | ||||||
![]() | retinol-binding protein / Retinol / Vitamin A / RBP | ||||||
Function / homology | ![]() all-trans-retinol binding / retinoic acid biosynthetic process / vitamin A metabolic process / retinoid binding / retinal binding / Retinoid cycle disease events / The canonical retinoid cycle in rods (twilight vision) / lipid homeostasis / fatty acid transport / Retinoid metabolism and transport ...all-trans-retinol binding / retinoic acid biosynthetic process / vitamin A metabolic process / retinoid binding / retinal binding / Retinoid cycle disease events / The canonical retinoid cycle in rods (twilight vision) / lipid homeostasis / fatty acid transport / Retinoid metabolism and transport / lipid droplet / fatty acid binding / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zanotti, G. / Vallese, F. / Berni, R. / Menozzi, I. | ||||||
![]() | ![]() Title: Structural and molecular determinants affecting the interaction of retinol with human CRBP1. Authors: Menozzi, I. / Vallese, F. / Polverini, E. / Folli, C. / Berni, R. / Zanotti, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 95.7 KB | Display | ![]() |
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PDB format | ![]() | 73.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 425 KB | Display | ![]() |
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Full document | ![]() | 425.5 KB | Display | |
Data in XML | ![]() | 9 KB | Display | |
Data in CIF | ![]() | 12.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ljbSC ![]() 5ljcC ![]() 5ljdC ![]() 5ljeC ![]() 5ljgC ![]() 5ljkC 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: 15855.162 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-NA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 40 % |
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Crystal grow | Temperature: 279 K / Method: vapor diffusion / pH: 5 Details: 0.2 M ammonium chloride, 0.1 M sodium acetate, 0.2 mM zinc chloride, pH 5,0, 20% PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 1, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00003 Å / Relative weight: 1 |
Reflection | Resolution: 1.52→47.6 Å / Num. obs: 20143 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Rmerge(I) obs: 0.031 / Net I/σ(I): 27.2 |
Reflection shell | Resolution: 1.52→1.61 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.468 / Mean I/σ(I) obs: 3.2 / % possible all: 93.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5LJB Resolution: 1.52→40.63 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.29 / Phase error: 18.96
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.52→40.63 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: 0.8622 Å / Origin y: 0.1681 Å / Origin z: -7.1266 Å
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Refinement TLS group | Selection details: ALL |