+Open data
-Basic information
Entry | Database: PDB / ID: 2ewf | ||||||
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Title | Crystal structure of the site-specific DNA nickase N.BspD6I | ||||||
Components | Nicking endonuclease N.BspD6I | ||||||
Keywords | HYDROLASE / helix-turn-helix / beta-alpha-barrel | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacillus sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.84 Å | ||||||
Authors | Kachalova, G.S. / Bartunik, H.D. / Artyukh, R.I. / Rogulin, E.A. / Perevyazova, T.A. / Zheleznaya, L.A. / Matvienko, N.I. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Structural analysis of the heterodimeric type IIS restriction endonuclease R.BspD6I acting as a complex between a monomeric site-specific nickase and a catalytic subunit. Authors: Kachalova, G.S. / Rogulin, E.A. / Yunusova, A.K. / Artyukh, R.I. / Perevyazova, T.A. / Matvienko, N.I. / Zheleznaya, L.A. / Bartunik, H.D. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2005 Title: Crystallization and preliminary crystallographic analysis of the site-specific DNA nickase Nb.BspD6I Authors: Kachalova, G.S. / Rogulin, E.A. / Artyukh, R.I. / Perevyazova, T.A. / Zheleznaya, L.A. / Matvienko, N.I. / Bartunik, H.D. #2: Journal: Biochemistry Mosc. / Year: 2003 Title: Cloning and sequencing of the gene of site-specific nickase N.BspD6I Authors: Perevyazova, T.A. / Rogulin, E.A. / Zheleznaya, L.A. / Matvienko, N.I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ewf.cif.gz | 149.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ewf.ent.gz | 115 KB | Display | PDB format |
PDBx/mmJSON format | 2ewf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ew/2ewf ftp://data.pdbj.org/pub/pdb/validation_reports/ew/2ewf | 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: 71702.078 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus sp. (bacteria) / Strain: D6 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10F / References: UniProt: Q8GCA3, UniProt: A3FEV7*PLUS | ||
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#2: Chemical | ChemComp-BR / #3: 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: 2.72 Å3/Da / Density % sol: 54.82 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.2 Details: 0.04 M KH2PO4, 16% (w/v) PEG 8000, 20% (v/v) glycerol, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 0.9198, 0.9200, 1.05 | ||||||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 25, 2005 | ||||||||||||
Radiation | Monochromator: graphite / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.84→20 Å / Num. obs: 67523 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.6 | ||||||||||||
Reflection shell | Resolution: 1.84→1.87 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.84→10 Å / Num. parameters: 22116 / Num. restraintsaints: 20045 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: ANISOTROPIC REFINEMENT
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Refine analyze | Num. disordered residues: 7 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 5358.79
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Refinement step | Cycle: LAST / Resolution: 1.84→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.84→1.87 Å / Redundancy reflection obs: 3131
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