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- PDB-4ybp: 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: 4ybp | ||||||
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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 after 24 hour incubation at 1.83 angstrom resolution - thermodynamic product - 1st 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 | ![]() | 49 KB | Display | ![]() |
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PDB format | ![]() | 32.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 640.9 KB | Display | ![]() |
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Full document | ![]() | 642 KB | Display | |
Data in XML | ![]() | 10 KB | Display | |
Data in CIF | ![]() | 13.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ybuC ![]() 4yceC ![]() 4ychC ![]() 4ydaC ![]() 4ydbC ![]() 4yfpC ![]() 4yfqC ![]() 4yfrC ![]() 4yggC ![]() 4yghC ![]() 4ygzC ![]() 4yh0C ![]() 4ykmC ![]() 4ykoC ![]() 2g7bS S: Starting model for refinement C: citing same article ( |
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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: 3.16 Å3/Da / Density % sol: 61.13 % |
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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: 0.97872 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.83→50 Å / Num. obs: 17982 / % possible obs: 100 % / Redundancy: 10.5 % / Biso Wilson estimate: 22.54 Å2 / Rmerge(I) obs: 0.071 / Χ2: 0.911 / Net I/av σ(I): 36.1 / Net I/σ(I): 8.1 / Num. measured all: 189007 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2G7B Resolution: 1.831→35.493 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 0.24 / Phase error: 20.12 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.964 Å2 / ksol: 0.34 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.831→35.493 Å
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Refine LS restraints |
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LS refinement shell |
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