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- PDB-4yce: Crystal structure of the R111K:Y134F:T54V:R132Q:P39Q:R59Y mutant ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4yce | ||||||
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Title | Crystal structure of the R111K:Y134F:T54V:R132Q:P39Q:R59Y mutant of human cellular retinoic acid binding proteinii with retinal at 1.95 angstrom- visible light irradiated crystal for 1 hour - 2nd cycle | ||||||
![]() | Cellular retinoic acid-binding protein 2 | ||||||
![]() | TRANSPORT PROTEIN / Protein Engineering / Photo switchable proteins / Retinal isomerization / Retinal Protonated Schiff Base pKa change | ||||||
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: 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 47.3 KB | Display | ![]() |
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PDB format | ![]() | 31.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 641 KB | Display | ![]() |
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Full document | ![]() | 641.5 KB | Display | |
Data in XML | ![]() | 9.6 KB | Display | |
Data in CIF | ![]() | 13 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ybpC ![]() 4ybuC ![]() 4ychC ![]() 4ydaC ![]() 4ydbC ![]() 4yfpC ![]() 4yfqC ![]() 4yfrC ![]() 4yggC ![]() 4yghC ![]() 4ygzC ![]() 4yh0C ![]() 4ykmC ![]() 4ykoC ![]() 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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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.) ![]() ![]() ![]() |
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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: 3.18 Å3/Da / Density % sol: 61.37 % |
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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: ![]() ![]() ![]() |
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: 1.95→50 Å / Num. obs: 14985 / % possible obs: 99.5 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 33.94 |
Reflection shell | Resolution: 1.95→1.98 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 4.69 / % possible all: 99.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2G7B Resolution: 1.953→35.591 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 0.32 / Phase error: 22.11 / 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: 36.773 Å2 / ksol: 0.326 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.953→35.591 Å
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Refine LS restraints |
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LS refinement shell |
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