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Yorodumi- PDB-1n3f: Crystal structure of I-CreI bound to a palindromic DNA sequence I... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1n3f | ||||||
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Title | Crystal structure of I-CreI bound to a palindromic DNA sequence II (palindrome of right side of wildtype DNA target sequence) | ||||||
Components |
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Keywords | HYDROLASE/DNA / Homing / endonuclease / LAGLIDADG / DNA recognition / HYDROLASE-DNA COMPLEX | ||||||
Function / homology | Function and homology information intron homing / chloroplast / endonuclease activity / Hydrolases; Acting on ester bonds / identical protein binding / metal ion binding Similarity search - Function | ||||||
Biological species | Chlamydomonas reinhardtii (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Chevalier, B. / Turmel, M. / Lemieux, C. / Monnat, R.J. / Stoddard, B.L. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 Title: Flexible DNA Target Site Recognition by Divergent Homing Endonuclease Isoschizomers I-CreI and I-MsoI Authors: Chevalier, B. / Turmel, M. / Lemieux, C. / Monnat, R.J. / Stoddard, B.L. | ||||||
History |
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Remark 999 | SEQUENCE THE DEPOSITORS BELIEVE THAT THE SEQUENCE GIVEN IN SWISSPROTT ENTRY P05725 IS INCORRECT FOR ...SEQUENCE THE DEPOSITORS BELIEVE THAT THE SEQUENCE GIVEN IN SWISSPROTT ENTRY P05725 IS INCORRECT FOR RESIDUES 42, 110, 111. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1n3f.cif.gz | 201.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1n3f.ent.gz | 152.2 KB | Display | PDB format |
PDBx/mmJSON format | 1n3f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n3/1n3f ftp://data.pdbj.org/pub/pdb/validation_reports/n3/1n3f | HTTPS FTP |
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-Related structure data
Related structure data | 1m5xC 1n3eC 1g9zS 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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2 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 4264.793 Da / Num. of mol.: 4 / Source method: obtained synthetically #2: DNA chain | Mass: 3060.016 Da / Num. of mol.: 4 / Source method: obtained synthetically #3: Protein | Mass: 18722.557 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: CR.LSU INTRON OF CHOROPLAST 23S RDNA GENE / Plasmid: pI-CreI / Production host: Escherichia coli (E. coli) / Strain (production host): BL21[DE3] References: UniProt: P05725, Hydrolases; Acting on ester bonds #4: Chemical | ChemComp-CA / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 44.59 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 25% PEG 400, 20 mM NaCl, 10 mM CaCl2, 100 mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.1 Å |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2→19.85 Å / Num. obs: 60035 / Biso Wilson estimate: 20.9 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1G9Z Resolution: 2→19.85 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1050567.39 / Data cutoff high rms absF: 1050567.39 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 54.4922 Å2 / ksol: 0.347962 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→19.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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