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Yorodumi- PDB-4ybu: Crystal structure of the R111K:Y134F:T54V:R132Q:P39Q:R59Y mutant ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ybu | ||||||
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Title | Crystal structure of the R111K:Y134F:T54V:R132Q:P39Q:R59Y mutant of human Cellular Retinoic Acid Binding ProteinII in complex with Retinal after 24 h incubation and 1 hour UV irradiation at 1.92 angstrom - 1st cycle | ||||||
Components | Cellular retinoic acid-binding protein 2 | ||||||
Keywords | TRANSPORT PROTEIN / Photoswitchable protein / Retinal isomerization / Retinal PSB / Protein engineering / Retinal iminium pKa change by isomerization | ||||||
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: 1.924 Å | ||||||
Authors | Nosrati, M. / Geiger, J.H. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2016 Title: A Photoisomerizing Rhodopsin Mimic Observed at Atomic Resolution. Authors: Nosrati, M. / Berbasova, T. / Vasileiou, C. / Borhan, B. / Geiger, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ybu.cif.gz | 46.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ybu.ent.gz | 31.4 KB | Display | PDB format |
PDBx/mmJSON format | 4ybu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yb/4ybu ftp://data.pdbj.org/pub/pdb/validation_reports/yb/4ybu | HTTPS FTP |
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-Related structure data
Related structure data | 4ybpC 4yceC 4ychC 4ydaC 4ydbC 4yfpC 4yfqC 4yfrC 4yggC 4yghC 4ygzC 4yh0C 4ykmC 4ykoC 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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Unit cell |
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-Components
#1: Protein | Mass: 15543.747 Da / Num. of mol.: 1 / Mutation: R111K, Y134F, T54V, P39Q, R132Q, R59Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CRABP2 / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P29373 |
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#2: Chemical | ChemComp-RET / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.16 Å3/Da / Density % sol: 61.04 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 6 / Details: 12% PEG3350, 8% Tacsimate, pH = 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 9, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9787 Å / Relative weight: 1 |
Reflection | Resolution: 1.92→50 Å / Num. obs: 15647 / % possible obs: 99.4 % / Redundancy: 10.5 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 34.86 |
Reflection shell | Resolution: 1.92→1.95 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.405 / Mean I/σ(I) obs: 3.65 / % possible all: 85 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2G7B Resolution: 1.924→45.081 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.17 / Phase error: 21.96 / 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: 40.762 Å2 / ksol: 0.349 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.924→45.081 Å
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Refine LS restraints |
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LS refinement shell |
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