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Yorodumi- PDB-6u32: Crystal structure of HaloTag bound to tetramethylrhodamine-HaloTa... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6u32 | ||||||
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Title | Crystal structure of HaloTag bound to tetramethylrhodamine-HaloTag ligand | ||||||
Components | HaloTag | ||||||
Keywords | HYDROLASE / HaloTag / Haloalkane dehalogenase / tetramethyrhodamine | ||||||
Function / homology | Chem-PVY Function and homology information | ||||||
Biological species | Rhodococcus sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å | ||||||
Authors | Berro, A.J. / Schreiter, E.R. | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2021 Title: The HaloTag as a general scaffold for far-red tunable chemigenetic indicators. Authors: Deo, C. / Abdelfattah, A.S. / Bhargava, H.K. / Berro, A.J. / Falco, N. / Farrants, H. / Moeyaert, B. / Chupanova, M. / Lavis, L.D. / Schreiter, E.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6u32.cif.gz | 140.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6u32.ent.gz | 107.8 KB | Display | PDB format |
PDBx/mmJSON format | 6u32.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6u32_validation.pdf.gz | 842.1 KB | Display | wwPDB validaton report |
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Full document | 6u32_full_validation.pdf.gz | 852.1 KB | Display | |
Data in XML | 6u32_validation.xml.gz | 16 KB | Display | |
Data in CIF | 6u32_validation.cif.gz | 22.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u3/6u32 ftp://data.pdbj.org/pub/pdb/validation_reports/u3/6u32 | HTTPS FTP |
-Related structure data
Related structure data | 6u2mC 5uy1S 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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Unit cell |
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-Components
#1: Protein | Mass: 33644.441 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodococcus sp. (bacteria) / Production host: Escherichia coli (E. coli) |
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#2: Chemical | ChemComp-PVY / |
#3: Chemical | ChemComp-CL / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.42 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2M MgCl2, 0.1M Tris pH 8.5, 20% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 2, 2015 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→58.435 Å / Num. all: 30022 / Num. obs: 30022 / % possible obs: 97 % / Redundancy: 5.8 % / Rpim(I) all: 0.044 / Rrim(I) all: 0.108 / Rsym value: 0.098 / Net I/av σ(I): 6.1 / Net I/σ(I): 11.2 / Num. measured all: 174075 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5UY1 Resolution: 1.8→58.43 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.959 / WRfactor Rfree: 0.19 / WRfactor Rwork: 0.1506 / FOM work R set: 0.8527 / SU B: 5.637 / SU ML: 0.084 / SU R Cruickshank DPI: 0.1109 / SU Rfree: 0.1084 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 96.23 Å2 / Biso mean: 28.574 Å2 / Biso min: 15.15 Å2
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Refinement step | Cycle: final / Resolution: 1.8→58.43 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 86.862 Å / Origin y: 59.99 Å / Origin z: 10.573 Å
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Refinement TLS group |
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