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Yorodumi- PDB-6uwj: Intermediate engineered variant of I-OnuI meganuclease with impro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6uwj | ||||||
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Title | Intermediate engineered variant of I-OnuI meganuclease with improved thermostability and partially altered specificity | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / Meganuclease / Homing Endonuclease / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | Homing endonucleases / Endonuclease I-creI / Roll / Alpha Beta / DNA / DNA (> 10) Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.852 Å | ||||||
Authors | Werther, R. / Stoddard, B.L. | ||||||
Funding support | United States, 1items
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Citation | Journal: Structure / Year: 2020 Title: Optimization of Protein Thermostability and Exploitation of Recognition Behavior to Engineer Altered Protein-DNA Recognition. Authors: Lambert, A.R. / Hallinan, J.P. / Werther, R. / Glow, D. / Stoddard, B.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6uwj.cif.gz | 108.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6uwj.ent.gz | 74.2 KB | Display | PDB format |
PDBx/mmJSON format | 6uwj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uw/6uwj ftp://data.pdbj.org/pub/pdb/validation_reports/uw/6uwj | HTTPS FTP |
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-Related structure data
Related structure data | 6uvwC 6uw0C 6uwgC 6uwhC 6uwkC 3qqyS 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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Unit cell |
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-Components
#1: Protein | Mass: 34144.758 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) | ||||
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#2: DNA chain | Mass: 8234.293 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||||
#3: DNA chain | Mass: 8359.414 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||||
#4: Chemical | ChemComp-CA / #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.86 Å3/Da / Density % sol: 33.82 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 100mM sodium acetate pH 6.0, 200mM calcium acetate, 35% PEG 400 |
-Data collection
Diffraction | Mean temperature: 108 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.977 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 25, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.977 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.85→50 Å / Num. obs: 33122 / % possible obs: 99.7 % / Redundancy: 11.3 % / Rmerge(I) obs: 0.035 / Rpim(I) all: 0.011 / Rrim(I) all: 0.037 / Χ2: 0.998 / Net I/σ(I): 20.2 / Num. measured all: 374757 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3QQY Resolution: 1.852→48.985 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.49
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 79.58 Å2 / Biso mean: 29.35 Å2 / Biso min: 14.75 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.852→48.985 Å
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Refine LS restraints |
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LS refinement shell |
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