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Yorodumi- PDB-5liq: The structure of C160S,C508S,C578S mutant of Nt.BspD6I nicking en... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5liq | ||||||
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Title | The structure of C160S,C508S,C578S mutant of Nt.BspD6I nicking endonuclease at 0.185 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: 1.85 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 | 5liq.cif.gz | 259 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5liq.ent.gz | 208 KB | Display | PDB format |
PDBx/mmJSON format | 5liq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5liq_validation.pdf.gz | 474.9 KB | Display | wwPDB validaton report |
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Full document | 5liq_full_validation.pdf.gz | 501.8 KB | Display | |
Data in XML | 5liq_validation.xml.gz | 47.7 KB | Display | |
Data in CIF | 5liq_validation.cif.gz | 66.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/li/5liq ftp://data.pdbj.org/pub/pdb/validation_reports/li/5liq | HTTPS FTP |
-Related structure data
Related structure data | 5lizC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 71653.891 Da / Num. of mol.: 2 / Mutation: C160S ; C508S; C578S Source method: isolated from a genetically manipulated source Details: three mutations : C160S C508S C578S / Source: (gene. exp.) Bacillus sp. (bacteria) / Plasmid: PET28B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8GCA3 #2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-PO4 / #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: 2.81 Å3/Da / Density % sol: 56.3 % / Description: long needle |
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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: 0.97623 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 4, 2016 / Details: MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97623 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→109.6 Å / Num. obs: 129563 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 34.15 Å2 / Rmerge(I) obs: 0.033 / Net I/σ(I): 18.7 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2EWF Resolution: 1.85→19.58 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.044 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.136 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.377 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→19.58 Å
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Refine LS restraints |
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