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- PDB-6ejv: Nuclease NucB from Bacillus licheniformis in sulphate free conditions -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ejv | ||||||||||||
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Title | Nuclease NucB from Bacillus licheniformis in sulphate free conditions | ||||||||||||
![]() | Nuclease | ||||||||||||
![]() | HYDROLASE / nuclease / DNAse / metal dependent | ||||||||||||
Function / homology | Deoxyribonuclease NucA/NucB / Deoxyribonuclease NucA/NucB / Nuclease![]() | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() | ||||||||||||
![]() | Stransky, J. / Dohnalek, J. / Oestergaard, L.A. | ||||||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 64.7 KB | Display | ![]() |
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PDB format | ![]() | 46.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 440.5 KB | Display | ![]() |
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Full document | ![]() | 440.6 KB | Display | |
Data in XML | ![]() | 14 KB | Display | |
Data in CIF | ![]() | 20.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ejsSC ![]() 6ejtC ![]() 6ejuC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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 EC3.1.21.1 / Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-TRS / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.12 M 1,6-Hexanediol 0.12 M 1-Butanol 0.12 M 1,2-Propanediol 0.12 M 2-Propanol 0.12 M 1,4-Butanediol 0.12 M 1,3-Propanediol 0.1 M Tris and Bicine pH 8.5 12.5 % v/v 2-Methyl- -2,4,- ...Details: 0.12 M 1,6-Hexanediol 0.12 M 1-Butanol 0.12 M 1,2-Propanediol 0.12 M 2-Propanol 0.12 M 1,4-Butanediol 0.12 M 1,3-Propanediol 0.1 M Tris and Bicine pH 8.5 12.5 % v/v 2-Methyl- -2,4,-pentanediol 12.5 % PEG 1000 12.5 % w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: LIQUID ANODE / Type: Excillum MetalJet D2+ 70 kV / Wavelength: 1.3418 Å |
Detector | Type: Bruker PHOTON II / Detector: PIXEL / Date: May 5, 2017 / Details: HELIOS MX |
Radiation | Monochromator: GOEBLE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.3418 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→45.5 Å / Num. obs: 24852 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 9.1 % / Biso Wilson estimate: 14.48 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.045 / Rrim(I) all: 0.101 / Net I/σ(I): 17.9 |
Reflection shell | Resolution: 1.75→1.78 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.872 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1354 / CC1/2: 0.78 / Rpim(I) all: 0.518 / Rrim(I) all: 1.018 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6EJS Resolution: 1.75→45.5 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.961 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.087 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: 71.45 Å2 / Biso mean: 22.3148 Å2 / Biso min: 11.17 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→45.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.795 Å / Total num. of bins used: 20
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