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- PDB-5y2y: Crystal structure of HaloTag (M175C) complexed with dansyl-PEG2-H... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5y2y | ||||||
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Title | Crystal structure of HaloTag (M175C) complexed with dansyl-PEG2-HaloTag ligand | ||||||
![]() | Haloalkane dehalogenase | ||||||
![]() | HYDROLASE / halotag / haloalkane dehalogenase / Dansyl ligand | ||||||
Function / homology | ![]() haloalkane dehalogenase / haloalkane dehalogenase activity / response to toxic substance Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lee, H. / Kang, M. / Rhee, H. / Lee, C. | ||||||
![]() | ![]() Title: Structure-guided synthesis of a protein-based fluorescent sensor for alkyl halides Authors: Kang, M.G. / Lee, H. / Kim, B.H. / Dunbayev, Y. / Seo, J.K. / Lee, C. / Rhee, H.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 137.7 KB | Display | ![]() |
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PDB format | ![]() | 105.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 959.4 KB | Display | ![]() |
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Full document | ![]() | 965.4 KB | Display | |
Data in XML | ![]() | 26.8 KB | Display | |
Data in CIF | ![]() | 37.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5y2xC ![]() 4kafS 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: 33716.398 Da / Num. of mol.: 2 Mutation: S2A, L47V, S58T, D78G, Y87F, L88M, C128F, A155T, E160K, A167V, A172T, K175C, C176G, K195N, A224E, N227D, E257K, T264A, H272N, Y273L, P291S, A292T Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.88 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.8M ammonium sulfate, 0.1M citric acid pH5.5. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 14, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.27→50 Å / Num. obs: 26399 / % possible obs: 98.4 % / Redundancy: 10.4 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 56.1 |
Reflection shell | Resolution: 2.27→2.31 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.073 / Mean I/σ(I) obs: 38.6 / % possible all: 88 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4KAF Resolution: 2.27→34.73 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 2.27→34.73 Å
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LS refinement shell | Resolution: 2.2742→2.3653 Å / Rfactor Rfree: 0.217 / Rfactor Rwork: 0.14 |