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Yorodumi- PDB-6eko: Crystal structure of Type IIP restriction endonuclease PfoI with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6eko | |||||||||
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Title | Crystal structure of Type IIP restriction endonuclease PfoI with cognate DNA | |||||||||
Components |
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Keywords | HYDROLASE / Restriction endonuclease / PD-(D/E)xK nuclease | |||||||||
Function / homology | type II site-specific deoxyribonuclease / type II site-specific deoxyribonuclease activity / DNA / DNA (> 10) / Restriction endonuclease PfoI Function and homology information | |||||||||
Biological species | Pseudomonas fluorescens (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.284 Å | |||||||||
Authors | Tamulaitiene, G. / Manakova, E. / Jovaisaite, V. / Grazulis, S. / Siksnys, V. | |||||||||
Funding support | Lithuania, 2items
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Citation | Journal: Nucleic Acids Res. / Year: 2019 Title: Unique mechanism of target recognition by PfoI restriction endonuclease of the CCGG-family. Authors: Tamulaitiene, G. / Manakova, E. / Jovaisaite, V. / Tamulaitis, G. / Grazulis, S. / Bochtler, M. / Siksnys, V. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6eko.cif.gz | 153.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6eko.ent.gz | 124 KB | Display | PDB format |
PDBx/mmJSON format | 6eko.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ek/6eko ftp://data.pdbj.org/pub/pdb/validation_reports/ek/6eko | 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: 35587.695 Da / Num. of mol.: 2 / Mutation: K187A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Variant: biovar 126 / Plasmid: pBAD24 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 References: UniProt: A0A452CST9*PLUS, type II site-specific deoxyribonuclease #2: DNA chain | Mass: 4257.754 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: Cognate oligoduplex with 3'-T-overhang and unpaired central recognition sequence base pair (C-C) Source: (synth.) Pseudomonas fluorescens (bacteria) #3: Chemical | ChemComp-CA / #4: 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: 2.8 Å3/Da / Density % sol: 56.09 % / Description: needles |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Reservoir: 20% PEG8000, 0.1M TrisHCl pH8.5, LiCl 0.2M and glycerol 10%. Protein-DNA complex concentration 5.3 mg/ml |
-Data collection
Diffraction | Mean temperature: 100 K Ambient temp details: cryo-protected by passing through mineral oil | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.96112,0.98010 | |||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 3, 2015 Details: Rh-coated Si mirrors: M1 collimating mirror, M2 toroidal focusing mirror | |||||||||
Radiation | Monochromator: Water-cooled double-crystal monochromator, Si(111) Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.28→47.96 Å / Num. obs: 36181 / % possible obs: 98.5 % / Redundancy: 13.5 % / Biso Wilson estimate: 27.3 Å2 / Rmerge(I) obs: 0.198 / Rpim(I) all: 0.058 / Rrim(I) all: 0.216 / Rsym value: 0.198 / Net I/σ(I): 11.6 | |||||||||
Reflection shell | Resolution: 2.28→2.41 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4683 / Rpim(I) all: 0.442 / % possible all: 89.8 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.284→47.96 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.99
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.284→47.96 Å
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Refine LS restraints |
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LS refinement shell |
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