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Yorodumi- PDB-5liz: The structure of Nt.BspD6I nicking endonuclease with all cysteine... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5liz | ||||||
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Title | The structure of Nt.BspD6I nicking endonuclease with all cysteines mutated by serine residues at 0.19 nm resolution . | ||||||
Components | Nicking endonuclease N.BspD6I | ||||||
Keywords | HYDROLASE / NICKING ENDONUCLEASE / RESTRICTION ENZYME HYDROLASE ACTIVITY'S MUTANT | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacillus sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å | ||||||
Authors | Kachalova, G.S. / Artyukh, R.I. / Perevyazova, T.A. / Yunusova, A.K. / Popov, A.N. / Bartunik, H.D. / Zheleznaya, L.A. | ||||||
Citation | Journal: To Be Published Title: Structural features of Cysteine residues mutation of the nicking endonuclease Nt.BspD6I. Authors: Kachalova, G.S. / Yunusova, A.K. / Popov, A.N. / Artyukh, R.I. / Perevyazova, T.A. / Bartunik, H.D. / Zheleznaya, L.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5liz.cif.gz | 138 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5liz.ent.gz | 105.9 KB | Display | PDB format |
PDBx/mmJSON format | 5liz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/li/5liz ftp://data.pdbj.org/pub/pdb/validation_reports/li/5liz | HTTPS FTP |
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-Related structure data
Related structure data | 5liqC 2ewfS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 71637.820 Da / Num. of mol.: 1 / Mutation: C11S C160S C508S C578S Source method: isolated from a genetically manipulated source Details: four mutations C11S C160S C508S C578S / Source: (gene. exp.) Bacillus sp. (bacteria) / Plasmid: PET28B / Production host: Escherichia coli (E. coli) / References: UniProt: Q8GCA3 |
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#2: Chemical | ChemComp-PO4 / |
#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: 2.86 Å3/Da / Density % sol: 57 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 16% PEG 8000 40MM POTASSIUM PHOSPHATE 20% GLYCEROL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.96862 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 15, 2016 / Details: MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96862 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→47.45 Å / Num. obs: 57969 / % possible obs: 99.7 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.129 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 1.93→2 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.636 / Mean I/σ(I) obs: 1.9 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2EWF Resolution: 1.93→19.55 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.08 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.142
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.405 Å2
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Refinement step | Cycle: 1 / Resolution: 1.93→19.55 Å
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Refine LS restraints |
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