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Yorodumi- PDB-5t2h: Engineered variant of I-OnuI meganuclease targeting the Human TCR... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5t2h | ||||||||||||
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Title | Engineered variant of I-OnuI meganuclease targeting the Human TCRa gene; harbors 43 point mutations relative to wild-type I-OnuI | ||||||||||||
Components |
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Keywords | HYDROLASE/DNA / Meganuclease / Engineered protein / DNA complex / Homing Endonuclease / HYDROLASE-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: 2.517 Å | ||||||||||||
Authors | Stoddard, B.L. / Werther, R. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Nucleic Acids Res. / Year: 2017 Title: Crystallographic analyses illustrate significant plasticity and efficient recoding of meganuclease target specificity. Authors: Werther, R. / Hallinan, J.P. / Lambert, A.R. / Havens, K. / Pogson, M. / Jarjour, J. / Galizi, R. / Windbichler, N. / Crisanti, A. / Nolan, T. / 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 | 5t2h.cif.gz | 104.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5t2h.ent.gz | 72.4 KB | Display | PDB format |
PDBx/mmJSON format | 5t2h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5t2h_validation.pdf.gz | 436.4 KB | Display | wwPDB validaton report |
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Full document | 5t2h_full_validation.pdf.gz | 437.9 KB | Display | |
Data in XML | 5t2h_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | 5t2h_validation.cif.gz | 17.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t2/5t2h ftp://data.pdbj.org/pub/pdb/validation_reports/t2/5t2h | HTTPS FTP |
-Related structure data
Related structure data | 5t2nC 5t2oC 3qqyS 5t2j C: citing same article (ref.) S: Starting model for refinement |
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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: 34775.266 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) / Strain (production host): BL21(DE3)RIL | ||
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#2: DNA chain | Mass: 7976.122 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||
#3: DNA chain | Mass: 7999.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 42.07 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 35% (v/v) Pentaerythritol ethoxylate (15/4 EO/OH), 50mM BIS-TRIS pH 6.5, 50mM ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 108 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.976 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 7, 2016 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(220) Asymmetric cut single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.52→50 Å / Num. obs: 15233 / % possible obs: 99.2 % / Redundancy: 13 % / Biso Wilson estimate: 54.84 Å2 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.029 / Rrim(I) all: 0.106 / Χ2: 0.887 / Net I/av σ(I): 25.694 / Net I/σ(I): 7.3 / Num. measured all: 198070 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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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: 2.517→41.77 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.45 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 118.78 Å2 / Biso mean: 54.6686 Å2 / Biso min: 24.95 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.517→41.77 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11
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