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- PDB-4i9s: Crystal Structure of the R111K:R132L:Y134F:T54V:R59W Mutant of th... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4i9s | ||||||
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Title | Crystal Structure of the R111K:R132L:Y134F:T54V:R59W Mutant of the Cellular Retinoic Acid Binding Protein Type II in Complex with All-Trans Retinal at 2.58 Angstrom Resolution | ||||||
![]() | Cellular retinoic acid-binding protein 2 | ||||||
![]() | TRANSPORT PROTEIN / protein engineering / wavelength regulation / pH sensing / pKa / retinylidene PSB / iminium | ||||||
Function / homology | ![]() positive regulation of collateral sprouting / retinoid binding / retinal binding / retinoic acid binding / embryonic forelimb morphogenesis / retinoic acid metabolic process / retinol binding / Signaling by Retinoic Acid / epidermis development / fatty acid transport ...positive regulation of collateral sprouting / retinoid binding / retinal binding / retinoic acid binding / embryonic forelimb morphogenesis / retinoic acid metabolic process / retinol binding / Signaling by Retinoic Acid / epidermis development / fatty acid transport / cyclin binding / fatty acid binding / regulation of DNA-templated transcription / endoplasmic reticulum / signal transduction / extracellular exosome / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nosrati, M. / Geiger, J.H. | ||||||
![]() | ![]() Title: Rational Design of a Colorimetric pH Sensor from a Soluble Retinoic Acid Chaperone. Authors: Berbasova, T. / Nosrati, M. / Vasileiou, C. / Wang, W. / Lee, K.S. / Yapici, I. / Geiger, J.H. / Borhan, B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 41.9 KB | Display | ![]() |
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PDB format | ![]() | 28.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 629.5 KB | Display | ![]() |
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Full document | ![]() | 631.3 KB | Display | |
Data in XML | ![]() | 8.3 KB | Display | |
Data in CIF | ![]() | 10.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4i9rC ![]() 4m6sC ![]() 4m7mC ![]() 2g7bS 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: 15520.796 Da / Num. of mol.: 1 / Mutation: R111K:R132L:Y134F:T54V:R59W Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-RET / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.21 Å3/Da / Density % sol: 61.64 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 16% w/v PEG8000, 0.04 M potassium phosphate monobasic, 20% v/v glycerol, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD |
Radiation | Monochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 2.58→29.023 Å / Num. obs: 6565 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2G7B Resolution: 2.58→29.023 Å / SU ML: 0.92 / σ(F): 1.09 / Phase error: 33.65 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.208 Å2 / ksol: 0.314 e/Å3 | ||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.58→29.023 Å
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Refine LS restraints |
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LS refinement shell |
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