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Yorodumi- PDB-5t8d: Engineered variant of I-OnuI meganuclease targeting the HIV integ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5t8d | |||||||||
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Title | Engineered variant of I-OnuI meganuclease targeting the HIV integrase gene; harbors 47 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: 2.15 Å | |||||||||
Authors | Stoddard, B.L. / Werther, R. / Lambert, A.R. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Protein Eng.Des.Sel. / Year: 2017 Title: Tuning DNA binding affinity and cleavage specificity of an engineered gene-targeting nuclease via surface display, flow cytometry and cellular analyses. Authors: Niyonzima, N. / Lambert, A.R. / Werther, R. / De Silva Feelixge, H. / Roychoudhury, P. / Greninger, A.L. / Stone, D. / Stoddard, B.L. / Jerome, K.R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5t8d.cif.gz | 112.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5t8d.ent.gz | 78.9 KB | Display | PDB format |
PDBx/mmJSON format | 5t8d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5t8d_validation.pdf.gz | 434.7 KB | Display | wwPDB validaton report |
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Full document | 5t8d_full_validation.pdf.gz | 435.9 KB | Display | |
Data in XML | 5t8d_validation.xml.gz | 16.4 KB | Display | |
Data in CIF | 5t8d_validation.cif.gz | 24.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t8/5t8d ftp://data.pdbj.org/pub/pdb/validation_reports/t8/5t8d | HTTPS FTP |
-Related structure data
Related structure data | 5v0qC 3qqyS 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: 34426.754 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: 8036.203 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||
#3: DNA chain | Mass: 7938.127 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: 2.44 Å3/Da / Density % sol: 49.58 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.2 M Ammonium sulfate, 0.1 M HEPES pH 7.0, 22.5% w/v Polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 108 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 3, 2016 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal, Si(111) liquid N2 cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.15→50 Å / Num. obs: 27792 / % possible obs: 99.9 % / Redundancy: 12.6 % / Biso Wilson estimate: 34.29 Å2 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.027 / Rrim(I) all: 0.097 / Χ2: 0.87 / Net I/av σ(I): 29.278 / Net I/σ(I): 6.7 / Num. measured all: 351202 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 2.15→44.381 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.33 / 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: 93.65 Å2 / Biso mean: 37.7676 Å2 / Biso min: 19.51 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.15→44.381 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: 10
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