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Yorodumi- PDB-4qgv: Crystal structure of the R132K:R111L mutant of Cellular Retinoic ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4qgv | ||||||
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Title | Crystal structure of the R132K:R111L mutant of Cellular Retinoic Acid Binding ProteinII complexed with a synthetic ligand (Merocyanine) at 1.73 angstrom resolution. | ||||||
Components | Cellular retinoic acid-binding protein 2 | ||||||
Keywords | PROTEIN BINDING / Protein Engineering / Protein Fluorescence Merocyanine dyes for fluorescent protein labeling / Fluorescent protein tag / Merocyanine Protonated Schiff Base / Iminium | ||||||
Function / homology | Function and homology information 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å | ||||||
Authors | Nosrati, M. / Yapici, I. / Geiger, J.H. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2015 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qgv.cif.gz | 73.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qgv.ent.gz | 54.1 KB | Display | PDB format |
PDBx/mmJSON format | 4qgv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qg/4qgv ftp://data.pdbj.org/pub/pdb/validation_reports/qg/4qgv | HTTPS FTP |
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-Related structure data
Related structure data | 3fepC 4qgwC 4qgxC 2g7bS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-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: 15509.753 Da / Num. of mol.: 2 / Mutation: R132K, R111L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CRABP2 / Plasmid: Pet17b / Production host: Escherichia coli (E. coli) / References: UniProt: P29373 #2: Chemical | ChemComp-LMC / ( | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.24 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M Bis Tris Propane, 0.2 M Sodium Fluoride, 16% PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.1272 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 14, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1272 Å / Relative weight: 1 |
Reflection | Resolution: 1.73→50 Å / Num. all: 134315 / Num. obs: 28219 / % possible obs: 95.2 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.045 / Rsym value: 0.035 / Net I/σ(I): 36.9 |
Reflection shell | Resolution: 1.73→1.77 Å / Rmerge(I) obs: 0.423 / Mean I/σ(I) obs: 3.4 / % possible all: 94.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 2G7B Resolution: 1.73→35.997 Å / SU ML: 0.48 / σ(F): 2 / Phase error: 27.61 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.872 Å2 / ksol: 0.4 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.73→35.997 Å
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Refine LS restraints |
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LS refinement shell |
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