+Open data
-Basic information
Entry | Database: PDB / ID: 3ool | ||||||
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Title | I-SceI complexed with C/G+4 DNA substrate | ||||||
Components |
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Keywords | HYDROLASE/DNA / homing endonuclease / intron homing / LAGLIDADG / Hydrolase-DNA complex | ||||||
Function / homology | Function and homology information Group II intron splicing / intron homing / mRNA cis splicing, via spliceosome / endonuclease activity / Hydrolases; Acting on ester bonds / mitochondrion Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Joshi, R. / Chen, J.-H. / Golden, B.L. / Gimble, F.S. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2011 Title: Evolution of I-SceI Homing Endonucleases with Increased DNA Recognition Site Specificity. Authors: Joshi, R. / Ho, K.K. / Tenney, K. / Chen, J.H. / Golden, B.L. / Gimble, F.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ool.cif.gz | 162.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ool.ent.gz | 123.9 KB | Display | PDB format |
PDBx/mmJSON format | 3ool.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oo/3ool ftp://data.pdbj.org/pub/pdb/validation_reports/oo/3ool | HTTPS FTP |
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-Related structure data
Related structure data | 3oorC 1r7mS 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: 27986.564 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: SceI,omega / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P03882, Hydrolases; Acting on ester bonds | ||
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#2: DNA chain | Mass: 7717.000 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Top strand of I-SceI C/G+4 DNA target | ||
#3: DNA chain | Mass: 7640.919 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Bottom strand of I-SceI C/G+4 DNA target | ||
#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: 2.26 Å3/Da / Density % sol: 45.62 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 4.7 Details: PEG400,CaCl2,NaOAc,DTT, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.979 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 8, 2009 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal cryo-cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→50 Å / Num. obs: 22091 / % possible obs: 84.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.051 / Χ2: 2.015 / Net I/σ(I): 18 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1R7M Resolution: 2.3→30.79 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.902 / Occupancy max: 1 / Occupancy min: 1 / SU B: 21.198 / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.315 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 119.27 Å2 / Biso mean: 43.9129 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→30.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.359 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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