+Open data
-Basic information
Entry | Database: PDB / ID: 6s58 | ||||||
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Title | AvaII restriction endonuclease in the absence of nucleic acids | ||||||
Components | Type II site-specific deoxyribonuclease | ||||||
Keywords | HYDROLASE / RESTRICTION ENDONUCLEASE / APO / SCANNING / SUBSTRATE / PRODUCT COMPLEX / RNA/DNA HYBRID / RNA/DNA HETERODUPLEX / A-DNA | ||||||
Function / homology | Type II restriction endonuclease SinI / SinI restriction endonuclease / type II site-specific deoxyribonuclease activity / DNA restriction-modification system / DNA binding / Type II site-specific deoxyribonuclease Function and homology information | ||||||
Biological species | Nostoc sp. PCC 7120 = FACHB-418 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å | ||||||
Authors | Kisiala, M. / Kowalska, M. / Korza, H. / Czapinska, H. / Bochtler, M. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2020 Title: Restriction endonucleases that cleave RNA/DNA heteroduplexes bind dsDNA in A-like conformation. Authors: Kisiala, M. / Kowalska, M. / Pastor, M. / Korza, H.J. / Czapinska, H. / Bochtler, M. #1: Journal: Nucleic Acids Res. / Year: 2010 Title: Sequence-specific cleavage of RNA by Type II restriction enzymes. Authors: Murray, I.A. / Stickel, S.K. / Roberts, R.J. #2: Journal: Nucleic Acids Res. / Year: 1980 Title: Cleavage of DNA.RNA hybrids by type II restriction enzymes. Authors: Molloy, P.L. / Symons, R.H. #3: 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. #4: Journal: Biophys. J. / Year: 2009 Title: Intrinsic dynamics of restriction endonuclease EcoO109I studied by molecular dynamics simulations and X-ray scattering data analysis. Authors: Oroguchi, T. / Hashimoto, H. / Shimizu, T. / Sato, M. / Ikeguchi, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6s58.cif.gz | 190.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6s58.ent.gz | 153.3 KB | Display | PDB format |
PDBx/mmJSON format | 6s58.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s5/6s58 ftp://data.pdbj.org/pub/pdb/validation_reports/s5/6s58 | HTTPS FTP |
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-Related structure data
Related structure data | 6s48C 6g3bS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 27161.797 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nostoc sp. PCC 7120 = FACHB-418 (bacteria) Gene: alr0933 / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / Variant (production host): ER2566 / References: UniProt: Q8YYB7 #2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-UNX / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.1 Å3/Da / Density % sol: 41.37 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.03 M CaCl2, 0.1 M MES/imidazole, pH 6.5, 12.5% v/v MPD, 12.5% w/v PEG 1000, 12.5% w/v PEG 3350 (Morpheus screen A4 condition with MgCl2 eliminated). |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å | |||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 16, 2019 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.35→53.3 Å / Num. obs: 37373 / % possible obs: 99.9 % / Redundancy: 3.3 % / Biso Wilson estimate: 54 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.065 / Rrim(I) all: 0.119 / Net I/σ(I): 5.5 | |||||||||||||||
Reflection shell | Resolution: 2.35→2.43 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.452 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3687 / CC1/2: 0.764 / Rpim(I) all: 0.309 / Rrim(I) all: 0.55 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6G3B Resolution: 2.32→51.37 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.942 / SU B: 7.9 / SU ML: 0.198 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.06 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 71.422 Å2
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Refinement step | Cycle: LAST / Resolution: 2.32→51.37 Å
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Refine LS restraints |
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