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- PDB-8vzy: Q108K:K40L:T51V:T53S:R58Y mutant of hCRBPII bound to synthetic fl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8vzy | ||||||
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Title | Q108K:K40L:T51V:T53S:R58Y mutant of hCRBPII bound to synthetic fluorophore TD-1V | ||||||
![]() | Retinol-binding protein 2 | ||||||
![]() | RETINOL BINDING PROTEIN / human cellular retinol binding protein II / hCRBPII / engineered protein / fluorescent protein | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Nossoni, Z. / Bingham, C.R. / Geiger, J.H. / Borhan, B. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Regulation of Emission via a Protein-Bound Fluorophore Authors: Santos, E.M. / Chandra, I. / Assar, Z. / Sheng, W. / Ghanbarpour, A. / Bingham, C.R. / 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 | ![]() | 135.2 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 682.3 KB | Display | ![]() |
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Full document | ![]() | 690.5 KB | Display | |
Data in XML | ![]() | 14.5 KB | Display | |
Data in CIF | ![]() | 20.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8vzxC ![]() 8vzzC ![]() 8w00C ![]() 8w02C ![]() 4qynS 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 15572.462 Da / Num. of mol.: 2 / Mutation: Q108K:K40L:T51V:T53S:R58Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-A1AEQ / ( | Mass: 271.377 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H17NOS / Feature type: SUBJECT OF INVESTIGATION #3: Chemical | ChemComp-ACT / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.08 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: PEG4000, ammonium acetate, sodium acetate / PH range: 4.0-4.8 / Temp details: room temperature |
-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: Apr 11, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.34→29.2 Å / Num. obs: 47165 / % possible obs: 79.62 % / Redundancy: 2 % / CC1/2: 0.837 / Net I/σ(I): 43.37 |
Reflection shell | Resolution: 1.34→1.37 Å / Num. unique obs: 12003 / CC1/2: 0.862 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 4QYN Resolution: 1.34→29.2 Å / Cross valid method: FREE R-VALUE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Displacement parameters | Biso mean: 29.11 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.34→29.2 Å
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Refine LS restraints |
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