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- PDB-8d6l: Q108K:K40L:T51C:T53A:R58L:Q38F:Q4F mutant of hCRBPII bound to syn... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8d6l | ||||||
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Title | Q108K:K40L:T51C:T53A:R58L:Q38F:Q4F mutant of hCRBPII bound to synthetic fluorophore CM1V | ||||||
![]() | Retinol-binding protein 2 | ||||||
![]() | TRANSPORT PROTEIN / hCRBPII | ||||||
Function / homology | ![]() vitamin A metabolic process / retinoid binding / retinal binding / retinol binding / epidermis development / fatty acid transport / Retinoid metabolism and transport / fatty acid binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bingham, C.R. / Geiger, J.H. / Borhan, B. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Light controlled reversible Michael addition of cysteine: a new tool for dynamic site-specific labeling of proteins. Authors: Maity, S. / Bingham, C. / Sheng, W. / Ehyaei, N. / Chakraborty, D. / Tahmasebi-Nick, S. / Kimmel, T.E. / Vasileiou, C. / Geiger, J.H. / Borhan, B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 47.1 KB | Display | ![]() |
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PDB format | ![]() | 30.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 718.7 KB | Display | ![]() |
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Full document | ![]() | 722.5 KB | Display | |
Data in XML | ![]() | 9.4 KB | Display | |
Data in CIF | ![]() | 11.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8d6hC ![]() 8d6nC ![]() 8db2C ![]() 8dn1C ![]() 4qypS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 15548.548 Da / Num. of mol.: 1 / Mutation: Q108K, K40L, T51C, T53A, R58L, Q38F, Q4F Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
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#2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-RH6 / ( | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.64 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 4 Details: PEG 4000, Ammonium Acetate, Sodium Acetate, pH 4.0 - 4.8 PH range: 4.0 - 4.8 |
-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: Jul 23, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1272 Å / Relative weight: 1 |
Reflection | Resolution: 1.69→33.63 Å / Num. obs: 13067 / % possible obs: 93.01 % / Redundancy: 9.8 % / Biso Wilson estimate: 40.52 Å2 / Rpim(I) all: 0.013 / Rrim(I) all: 0.041 / Net I/σ(I): 13067 |
Reflection shell | Resolution: 1.69→1.749 Å / Num. unique obs: 1152 / CC1/2: 0.923 / Rpim(I) all: 0.205 / Rrim(I) all: 0.488 / % possible all: 81.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4QYP Resolution: 1.69→33.62 Å / SU ML: 0.3284 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 36.6574 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.85 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.69→33.62 Å
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Refine LS restraints |
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LS refinement shell |
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