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Yorodumi- PDB-5y2y: Crystal structure of HaloTag (M175C) complexed with dansyl-PEG2-H... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5y2y | ||||||
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Title | Crystal structure of HaloTag (M175C) complexed with dansyl-PEG2-HaloTag ligand | ||||||
Components | Haloalkane dehalogenase | ||||||
Keywords | HYDROLASE / halotag / haloalkane dehalogenase / Dansyl ligand | ||||||
Function / homology | Function and homology information haloalkane dehalogenase / haloalkane dehalogenase activity / response to toxic substance Similarity search - Function | ||||||
Biological species | Rhodococcus sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å | ||||||
Authors | Lee, H. / Kang, M. / Rhee, H. / Lee, C. | ||||||
Citation | Journal: Chem. Commun. (Camb.) / Year: 2017 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5y2y.cif.gz | 137.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5y2y.ent.gz | 105.3 KB | Display | PDB format |
PDBx/mmJSON format | 5y2y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y2/5y2y ftp://data.pdbj.org/pub/pdb/validation_reports/y2/5y2y | HTTPS FTP |
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-Related structure data
Related structure data | 5y2xC 4kafS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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.) Rhodococcus sp. (bacteria) / Gene: dhaA / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0A3G3, haloalkane dehalogenase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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 |