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Yorodumi- PDB-7rce: Third stage reengineered variant of I-OnuI with specificity enhan... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7rce | ||||||||||||
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Title | Third stage reengineered variant of I-OnuI with specificity enhancing substitutions | ||||||||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / meganuclease / gene editing / protein engineering / DNA BINDING PROTEIN-DNA complex | ||||||||||||
Function / homology | DNA / DNA (> 10) Function and homology information | ||||||||||||
Biological species | Synthetic construct (others) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.42 Å | ||||||||||||
Authors | Ubilla-Rodriguez, N.C. / Werther, R.A. / Stoddard, B.L. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: To Be Published Title: Characterization of the stepwise engineering and optimization of a retargeted DNA binding protein and gene-editing meganuclease Authors: Werther, R.A. / Ubilla-Rodriguez, N.C. / Smiley, A.T. / Havens, K. / Lambert, A.R. / 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 | 7rce.cif.gz | 184.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7rce.ent.gz | 138.4 KB | Display | PDB format |
PDBx/mmJSON format | 7rce.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7rce_validation.pdf.gz | 427.2 KB | Display | wwPDB validaton report |
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Full document | 7rce_full_validation.pdf.gz | 429.5 KB | Display | |
Data in XML | 7rce_validation.xml.gz | 13.2 KB | Display | |
Data in CIF | 7rce_validation.cif.gz | 17.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rc/7rce ftp://data.pdbj.org/pub/pdb/validation_reports/rc/7rce | HTTPS FTP |
-Related structure data
Related structure data | 7rccC 7rcdC 7rcfC 7rcgC 3qqyS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 34983.344 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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-DNA chain , 2 types, 2 molecules BC
#2: DNA chain | Mass: 8064.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others) |
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#3: DNA chain | Mass: 7917.066 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others) |
-Non-polymers , 3 types, 12 molecules
#4: Chemical | #5: Chemical | ChemComp-NA / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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Sequence details | The wild type homing endonuclease was extensively engineered to generate I-OnuI_e-hPD1-d. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 100mM TRIS pH 6.0, 50mM ammonium sulfate, 35% pentaerythritol ethoxylate 15/4 EO/OH |
-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: 0.977408 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 11, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.977408 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.42→50 Å / Num. obs: 16849 / % possible obs: 99.6 % / Redundancy: 10.9 % / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.026 / Rrim(I) all: 0.088 / Χ2: 1.045 / Net I/σ(I): 13 / Num. measured all: 182909 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 2.42→41.74 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.99 / 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: 166.65 Å2 / Biso mean: 83.3682 Å2 / Biso min: 33.46 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.42→41.74 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12
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Refinement TLS params. | Method: refined / Origin x: -7.5629 Å / Origin y: -0.0095 Å / Origin z: 27.3186 Å
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Refinement TLS group |
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