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Yorodumi- PDB-1m5x: Crystal structure of the homing endonuclease I-MsoI bound to its ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1m5x | ||||||
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Title | Crystal structure of the homing endonuclease I-MsoI bound to its DNA substrate | ||||||
Components |
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Keywords | HYDROLASE/DNA / LAGLIDADG / HYDROLASE-DNA COMPLEX | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Monomastix sp. (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1m5x.cif.gz | 111.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1m5x.ent.gz | 81.5 KB | Display | PDB format |
PDBx/mmJSON format | 1m5x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1m5x_validation.pdf.gz | 457.1 KB | Display | wwPDB validaton report |
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Full document | 1m5x_full_validation.pdf.gz | 469.2 KB | Display | |
Data in XML | 1m5x_validation.xml.gz | 19.1 KB | Display | |
Data in CIF | 1m5x_validation.cif.gz | 27.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m5/1m5x ftp://data.pdbj.org/pub/pdb/validation_reports/m5/1m5x | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 7419.792 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: target DNA (Watson strand) | ||||
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#2: DNA chain | Mass: 7321.716 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: target DNA (Crick strand) | ||||
#3: Protein | Mass: 19471.416 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Monomastix sp. (plant) / Strain: OKE-1 / Plasmid: pI-MsoI / Production host: Escherichia coli (E. coli) / Strain (production host): BL21[DE3] / References: UniProt: Q8WKW7, UniProt: C0JWR6*PLUS #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: 2.04 Å3/Da / Density % sol: 39.58 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 400, sodium chloride, calcium chloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 18 ℃ / Method: vapor diffusion, hanging drop / PH range low: 7.9 / PH range high: 7.3 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Detector: CCD / Date: Mar 5, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→50 Å / Num. obs: 20335 / % possible obs: 97.6 % / Biso Wilson estimate: 23.2 Å2 / Rmerge(I) obs: 0.035 / Net I/σ(I): 26.1 |
Reflection shell | Resolution: 2.25→2.39 Å / Rmerge(I) obs: 0.076 / Mean I/σ(I) obs: 9.79 / % possible all: 96.9 |
Reflection | *PLUS Num. obs: 19849 / % possible obs: 97.5 % / Num. measured all: 38547 / Rmerge(I) obs: 0.03 |
Reflection shell | *PLUS % possible obs: 96.9 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: poly ananine I-CreI/DNA complex Resolution: 2.25→19.96 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 881264.79 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.7588 Å2 / ksol: 0.352117 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.3 Å2
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Refine analyze | Luzzati coordinate error free: 0.35 Å / Luzzati sigma a free: 0.36 Å | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→19.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.39 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 50 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.253 / Rfactor Rwork: 0.218 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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