+Open data
-Basic information
Entry | Database: PDB / ID: 6eju | ||||||||||||
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Title | Nuclease NucB from Bacillus licheniformis in P1 space group | ||||||||||||
Components | Nuclease | ||||||||||||
Keywords | HYDROLASE / nuclease / DNAse / metal dependent | ||||||||||||
Function / homology | Deoxyribonuclease NucA/NucB / Deoxyribonuclease NucA/NucB / Nuclease Function and homology information | ||||||||||||
Biological species | Bacillus licheniformis (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||||||||
Authors | Stransky, J. / Dohnalek, J. / Oestergaard, L.A. | ||||||||||||
Funding support | Czech Republic, 3items
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Citation | Journal: To Be Published Title: Structure of novel nuclease NucB from Bacillus licheniformis Authors: Stransky, J. / Dohnalek, J. / Oestergaard, L.H. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6eju.cif.gz | 62.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6eju.ent.gz | 44.4 KB | Display | PDB format |
PDBx/mmJSON format | 6eju.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6eju_validation.pdf.gz | 435.3 KB | Display | wwPDB validaton report |
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Full document | 6eju_full_validation.pdf.gz | 435.5 KB | Display | |
Data in XML | 6eju_validation.xml.gz | 13.2 KB | Display | |
Data in CIF | 6eju_validation.cif.gz | 18.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ej/6eju ftp://data.pdbj.org/pub/pdb/validation_reports/ej/6eju | HTTPS FTP |
-Related structure data
Related structure data | 6ejsC 6ejtSC 6ejvC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 12001.333 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: putative EC 3.1.21.1 / Source: (gene. exp.) Bacillus licheniformis (bacteria) / Gene: nucB, BL00126 / Production host: Bacillus subtilis (bacteria) / References: UniProt: Q65J43 #2: Chemical | ChemComp-SO4 / #3: 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: 2.4 Å3/Da / Density % sol: 47.6 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 1.8 M ammonium sulfate, 0.1 M sodium acetate pH 4.6 0.02 M MnCl2 (soaked) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 1.823 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 4, 2013 |
Radiation | Monochromator: 2 MIRROR AND DOUBLE-CRYSTAL MONCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.823 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→46.47 Å / Num. obs: 15502 / % possible obs: 90.1 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 21.43 Å2 / CC1/2: 0.979 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.034 / Rrim(I) all: 0.056 / Net I/σ(I): 19.1 |
Reflection shell | Resolution: 1.9→1.94 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.182 / Mean I/σ(I) obs: 5.4 / Num. unique obs: 722 / CC1/2: 0.639 / Rpim(I) all: 0.148 / Rrim(I) all: 0.236 / % possible all: 64.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6ejt Resolution: 1.9→46.47 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.953 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.188 / ESU R Free: 0.13 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 63.54 Å2 / Biso mean: 25.4376 Å2 / Biso min: 1 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→46.47 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.95 Å / Total num. of bins used: 20
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