+Open data
-Basic information
Entry | Database: PDB / ID: 5omt | ||||||
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Title | Endonuclease NucB | ||||||
Components | NucB | ||||||
Keywords | HYDROLASE / Endonuclease / biofilm / Bacillus subtilis / DNA | ||||||
Function / homology | Deoxyribonuclease NucA/NucB / Deoxyribonuclease NucA/NucB / NucB Function and homology information | ||||||
Biological species | Bacillus licheniformis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.35 Å | ||||||
Authors | Basle, A. / Lewis, R.J. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2018 Title: Crystal structure of NucB, a biofilm-degrading endonuclease. Authors: Basle, A. / Hewitt, L. / Koh, A. / Lamb, H.K. / Thompson, P. / Burgess, J.G. / Hall, M.J. / Hawkins, A.R. / Murray, H. / Lewis, R.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5omt.cif.gz | 56.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5omt.ent.gz | 43.7 KB | Display | PDB format |
PDBx/mmJSON format | 5omt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5omt_validation.pdf.gz | 405.8 KB | Display | wwPDB validaton report |
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Full document | 5omt_full_validation.pdf.gz | 405.8 KB | Display | |
Data in XML | 5omt_validation.xml.gz | 7.3 KB | Display | |
Data in CIF | 5omt_validation.cif.gz | 9.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/om/5omt ftp://data.pdbj.org/pub/pdb/validation_reports/om/5omt | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 12014.332 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus licheniformis (bacteria) / Gene: nucB / Production host: Bacillus subtilis (bacteria) / References: UniProt: F1BV52 |
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#2: 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: 2.49 Å3/Da / Density % sol: 50.62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100 mM MES pH6.5 12% PEG 20000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 14, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→44.56 Å / Num. obs: 27361 / % possible obs: 100 % / Redundancy: 7.8 % / CC1/2: 0.991 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 1.35→1.37 Å / Redundancy: 7.7 % / Mean I/σ(I) obs: 3.6 / Num. unique obs: 1316 / CC1/2: 0.944 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.35→44.56 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.528 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.048 / ESU R Free: 0.049 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.443 Å2
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Refinement step | Cycle: 1 / Resolution: 1.35→44.56 Å
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Refine LS restraints |
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