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- PDB-4ydb: 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: 4ydb | ||||||
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Title | Crystal structure of the R111K:Y134F:T54V:R132Q:P39Q:R59Y mutant of human Cellular Retinoic Acid Binding Protein II in complex with Retinal at 2.03 angstrom -UV irradiated crystal- 3rd cycle | ||||||
![]() | Cellular retinoic acid-binding protein 2 | ||||||
![]() | ![]() ![]() ![]() | ||||||
Function / homology | ![]() positive regulation of collateral sprouting / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() 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 | ![]() | 44.9 KB | Display | ![]() |
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PDB format | ![]() | 29.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4ybpC ![]() 4ybuC ![]() 4yceC ![]() 4ychC ![]() 4ydaC ![]() 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, R132Q, P39Q, 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: 3.21 Å3/Da / Density % sol: 61.63 % |
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, hanging drop / 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 300 mm CCD / Detector: CCD / Date: Jul 13, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.03→50 Å / Num. obs: 13508 / % possible obs: 100 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 38.81 |
Reflection shell | Resolution: 2.03→2.07 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 4.38 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 2G7B Resolution: 2.03→35.697 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.17 / 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: 54.19 Å2 / ksol: 0.377 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.03→35.697 Å
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Refine LS restraints |
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LS refinement shell |
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