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Yorodumi- PDB-1wtd: Crystal structure of type II restrcition endonuclease, EcoO109I D... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wtd | ||||||
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Title | Crystal structure of type II restrcition endonuclease, EcoO109I DNA-free form | ||||||
Components | EcoO109IR | ||||||
Keywords | HYDROLASE / RESTRICTION ENDONUCLEASE / DNA-FREE FROM | ||||||
Function / homology | Function and homology information type ii restriction endonuclease, domain 1 / type ii restriction endonuclease, domain 1 / type ii restriction endonuclease, domain 2 / type ii restriction endonuclease, domain 2 / Restriction endonuclease EcoO109IR, catalytic domain superfamily / Restriction endonuclease type II-like / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.401 Å | ||||||
Authors | Hashimoto, H. / Shimizu, T. / Imasaki, T. / Kato, M. / Shichijo, N. / Kita, K. / Sato, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: Crystal structures of type II restriction endonuclease EcoO109I and its complex with cognate DNA Authors: Hashimoto, H. / Shimizu, T. / Imasaki, T. / Kato, M. / Shichijo, N. / Kita, K. / Sato, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wtd.cif.gz | 116 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wtd.ent.gz | 90.8 KB | Display | PDB format |
PDBx/mmJSON format | 1wtd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wt/1wtd ftp://data.pdbj.org/pub/pdb/validation_reports/wt/1wtd | HTTPS FTP |
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-Related 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: 31481.975 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 References: UniProt: Q9RPJ3, type II site-specific deoxyribonuclease #2: Chemical | ChemComp-GOL / #3: 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: 2.7 Å3/Da / Density % sol: 54 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 4000, potassium chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1.0000, 1.0082, 1.0089, 0.9 | |||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD | |||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.4→20 Å / Num. all: 26765 / Num. obs: 26765 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 | |||||||||||||||
Reflection shell | Resolution: 2.4→2.49 Å / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.401→20 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.896 / Cross valid method: THROUGHOUT / ESU R: 0.441 / ESU R Free: 0.298 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.495 Å2
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Refinement step | Cycle: LAST / Resolution: 2.401→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.401→2.463 Å / Total num. of bins used: 20
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