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- PDB-6mqj: Crystal Structure of the All-Trans Retinal bound R111K:Y134F:T54V... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6mqj | ||||||
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Title | Crystal Structure of the All-Trans Retinal bound R111K:Y134F:T54V:R132Q:P39Y:R59Y:L121Q mutant of Human Cellular Retinoic Acid Binding Protein II Irradiated with 532 nm Laser for 10 minutes at 2.1 Angstrom Resolution | ||||||
![]() | Cellular retinoic acid-binding protein 2 | ||||||
![]() | LIPID BINDING PROTEIN / iLBP / Rhodopsin mimic | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Ghanbarpour, A. / Geiger, J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Mimicking Microbial Rhodopsin Isomerization in a Single Crystal. Authors: Ghanbarpour, A. / Nairat, M. / Nosrati, M. / Santos, E.M. / Vasileiou, C. / Dantus, M. / 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 | ![]() | 45.4 KB | Display | ![]() |
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PDB format | ![]() | 30.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 633.6 KB | Display | ![]() |
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Full document | ![]() | 635 KB | Display | |
Data in XML | ![]() | 8.3 KB | Display | |
Data in CIF | ![]() | 10.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6mopC ![]() 6moqC ![]() 6morC ![]() 6movC ![]() 6moxC ![]() 6mpkC ![]() 6mqiC ![]() 6mqwC ![]() 6mqxC ![]() 6mqyC ![]() 6mqzC ![]() 6mr0C ![]() 4yfpS 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: 15593.763 Da / Num. of mol.: 1 / Mutation: R111K,Y134F,T54V,R132Q,P39Y,R59Y,L121Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: Bacterial expression vector pBEN1-SGC (others) References: UniProt: P29373 |
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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: 3.23 Å3/Da / Density % sol: 61.9 % / Description: Hexagonal |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: PEG3350, DL-malic acid |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 4, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97626 Å / Relative weight: 1 |
Reflection | Resolution: 2.125→45.587 Å / Num. obs: 11843 / % possible obs: 99.72 % / Redundancy: 8.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.3 |
Reflection shell | Resolution: 2.125→2.201 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.515 / Num. unique obs: 1167 / Rrim(I) all: 0.685 / % possible all: 98.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4YFP Resolution: 2.125→45.587 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.48 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.125→45.587 Å
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Refine LS restraints |
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LS refinement shell |
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