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- PDB-4qgx: Crystal structure of the R132K:R111L:L121E mutant of Cellular Ret... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4qgx | ||||||
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Title | Crystal structure of the R132K:R111L:L121E mutant of Cellular Retinoic Acid Binding ProteinII complexed with a synthetic ligand (Merocyanine) at 1.47 angstrom resolution | ||||||
![]() | Cellular retinoic acid-binding protein 2 | ||||||
![]() | PROTEIN BINDING / Protein Engineering / Protein Fluorescence / Merocyanine dyes for fluorescent protein labeling / Fluorescent protein tag / Merocyanine Protonated Schiff Base 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. / Yapici, I. / Geiger, J.H. | ||||||
![]() | ![]() Title: "Turn-on" protein fluorescence: in situ formation of cyanine dyes. Authors: Yapici, I. / Lee, K.S. / Berbasova, T. / Nosrati, M. / Jia, X. / Vasileiou, C. / Wang, W. / Santos, E.M. / 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 | ![]() | 76.6 KB | Display | ![]() |
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PDB format | ![]() | 56.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 706.9 KB | Display | ![]() |
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Full document | ![]() | 708.3 KB | Display | |
Data in XML | ![]() | 16.3 KB | Display | |
Data in CIF | ![]() | 24 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3fepC ![]() 4qgvC ![]() 4qgwC ![]() 2g7bS C: citing same article ( S: Starting model for refinement |
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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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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 15525.708 Da / Num. of mol.: 2 / Mutation: R132K, R111L, L121E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-LMC / ( | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.07 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M bis Tris Propane, 0.2M Sodium Floride, 16% PEG3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 8, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.47→50 Å / Num. all: 174571 / Num. obs: 45647 / % possible obs: 96.5 % / Redundancy: 4 % / Rmerge(I) obs: 0.045 / Rsym value: 0.034 / Net I/σ(I): 31.5 |
Reflection shell | Resolution: 1.47→1.5 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.402 / Mean I/σ(I) obs: 2.8 / Rsym value: 0.371 / % possible all: 93.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 2G7B Resolution: 1.471→35.239 Å / SU ML: 0.44 / σ(F): 1.99 / Phase error: 22.73 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.962 Å2 / ksol: 0.375 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.471→35.239 Å
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Refine LS restraints |
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LS refinement shell |
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