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- PDB-4ygz: CRYSTAL STRUCTURE OF THE R111K:Y134F:T54V:R132Q:P39Y:R59Y MUTANT ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ygz | ||||||
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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 AT 2.06 ANGSTROM RESOLUTION - VISIBLE LIGHT IRRADIATED CRYSTAL -3RD CYCLE | ||||||
![]() | Cellular retinoic acid-binding protein 2 | ||||||
![]() | TRANSPORT PROTEIN / Photo swithcable protein / Retinal isomerization / Retinal iminium protonated Schiff base pKa change / protein engineering | ||||||
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 / signal transduction / endoplasmic reticulum / extracellular exosome / nucleoplasm / nucleus / cytosol / cytoplasm 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 | ![]() | 46 KB | Display | ![]() |
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PDB format | ![]() | 30.6 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 ![]() 4ydbC ![]() 4yfpC ![]() 4yfqC ![]() 4yfrC ![]() 4yggC ![]() 4yghC ![]() 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: 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.) ![]() ![]() ![]() |
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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: 3.24 Å3/Da / Density % sol: 62 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: 12% PEG3350, 0.1M Malonate 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: Jul 13, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2.06→50 Å / Num. obs: 13048 / % possible obs: 99.9 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.068 / Rsym value: 0.053 / Net I/σ(I): 40.72 |
Reflection shell | Resolution: 2.06→2.1 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.533 / Mean I/σ(I) obs: 5.12 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2G7B Resolution: 2.06→45.526 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 24.55 / 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: 36.115 Å2 / ksol: 0.328 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.06→45.526 Å
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Refine LS restraints |
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LS refinement shell |
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