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- PDB-6y8p: Crystal structure of SNAP-tag labeled with a benzyl-tetramethylrh... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6y8p | ||||||
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Title | Crystal structure of SNAP-tag labeled with a benzyl-tetramethylrhodamine fluorophore | ||||||
![]() | O6-alkylguanine-DNA alkyltransferase mutant | ||||||
![]() | TRANSFERASE / SNAP-tag / self-labeling protein / tetramethylrhodamine / synthetic fluorophore | ||||||
Function / homology | ![]() methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity / methylation / DNA repair / DNA binding / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gotthard, G. / Tanzer, T. / Johnsson, K. / Hiblot, J. | ||||||
![]() | ![]() Title: Kinetic and Structural Characterization of the Self-Labeling Protein Tags HaloTag7, SNAP-tag, and CLIP-tag. Authors: Wilhelm, J. / Kuhn, S. / Tarnawski, M. / Gotthard, G. / Tunnermann, J. / Tanzer, T. / Karpenko, J. / Mertes, N. / Xue, L. / Uhrig, U. / Reinstein, J. / Hiblot, J. / Johnsson, K. #1: ![]() Title: Kinetic and structural characterization of the self-labeling protein tags HaloTag7, SNAP-tag and CLIP-tag Authors: Wilhelm, J. / Kuhn, S. / Tarnawski, M. / Gotthard, G. / Tunnermann, J. / Tanzer, T. / Karpenko, J. / Mertes, N. / Xue, L. / Uhrig, U. / Reinstein, J. / Hiblot, J. / Johnsson, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 85.7 KB | Display | ![]() |
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PDB format | ![]() | 62.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6y7aC ![]() 6y7bC ![]() 6zccC ![]() 3l00S 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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Unit cell |
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Components
#1: Protein | Mass: 18951.752 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-OGQ / [ |
#4: Chemical | ChemComp-EDO / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.48 Å3/Da / Density % sol: 61.24 % / Description: Red hexaedral crystals |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 100 mM Na HEPES pH 7.5 25% PEG 8000 10 mg/mL protein 100 nl:100 nL |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 3, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→48.98 Å / Num. obs: 11154 / % possible obs: 99.94 % / Redundancy: 10.7 % / CC1/2: 0.999 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2.3→2.382 Å / Num. unique obs: 1087 / CC1/2: 0.193 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3l00 Resolution: 2.3→48.98 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 37.4
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 143.77 Å2 / Biso mean: 73.1096 Å2 / Biso min: 31.06 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.3→48.98 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Origin x: 16.4644 Å / Origin y: -5.4937 Å / Origin z: 2.3287 Å
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Refinement TLS group |
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