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Yorodumi- PDB-4yfp: CRYSTAL STRUCTURE OF THE R111K:Y134F:T54V:R132Q:P39Y:R59Y MUTANT ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4yfp | ||||||
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Title | CRYSTAL STRUCTURE OF THE R111K:Y134F:T54V:R132Q:P39Y:R59Y MUTANT OF HUMAN CELLULAR RETINOIC ACID BINDING PROTEIN II WITH RETINAL AFTER 20 MINUTES INCUBATION AT 1.95 ANGSTROM RESOLUTION-Kinetic Product | ||||||
Components | Cellular retinoic acid-binding protein 2 | ||||||
Keywords | TRANSPORT PROTEIN / Photo switchable proteins / Retinal isomerization / Retinal Protonated Schiff Base pKa change / Protein engineering | ||||||
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 / cyclin binding / epidermis development ...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 / cyclin binding / epidermis development / fatty acid transport / fatty acid binding / regulation of DNA-templated transcription / signal transduction / endoplasmic reticulum / extracellular exosome / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.951 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 | 4yfp.cif.gz | 77.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4yfp.ent.gz | 57.6 KB | Display | PDB format |
PDBx/mmJSON format | 4yfp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4yfp_validation.pdf.gz | 656.8 KB | Display | wwPDB validaton report |
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Full document | 4yfp_full_validation.pdf.gz | 658.5 KB | Display | |
Data in XML | 4yfp_validation.xml.gz | 9.3 KB | Display | |
Data in CIF | 4yfp_validation.cif.gz | 12.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yf/4yfp ftp://data.pdbj.org/pub/pdb/validation_reports/yf/4yfp | HTTPS FTP |
-Related structure data
Related structure data | 4ybpC 4ybuC 4yceC 4ychC 4ydaC 4ydbC 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: 15578.792 Da / Num. of mol.: 1 / Mutation: R111K, Y134F, T54V, R132Q, P39Y, 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: 3.22 Å3/Da / Density % sol: 61.76 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 12% PEG3350, 0.1M Malonate 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: Oct 14, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9787 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. obs: 15215 / % possible obs: 99.5 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.094 / Rsym value: 0.08 / Net I/σ(I): 34.6 |
Reflection shell | Resolution: 1.95→1.98 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.639 / Mean I/σ(I) obs: 3 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2G7B Resolution: 1.951→35.709 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 19.45 / 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: 44.719 Å2 / ksol: 0.333 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.951→35.709 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: -23.4834 Å / Origin y: 12.5026 Å / Origin z: -4.8679 Å
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Refinement TLS group | Selection details: all |