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- PDB-5fbg: S1 nuclease from Aspergillus oryzae, mutant D65N, in complex with... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5fbg | ||||||||||||
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Title | S1 nuclease from Aspergillus oryzae, mutant D65N, in complex with phosphate, 2'-deoxycytidine and 2'-deoxyguanosine. | ||||||||||||
![]() | Nuclease S1 | ||||||||||||
![]() | HYDROLASE / Endonuclease / Zinc dependent / Complex / mutant | ||||||||||||
Function / homology | ![]() Aspergillus nuclease S1 / nuclease activity / DNA catabolic process / endonuclease activity / nucleic acid binding / metal ion binding Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Koval, T. / Oestergaard, L.H. / Dohnalek, J. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural and Catalytic Properties of S1 Nuclease from Aspergillus oryzae Responsible for Substrate Recognition, Cleavage, Non-Specificity, and Inhibition. Authors: Koval, T. / stergaard, L.H. / Lehmbeck, J. / Nrgaard, A. / Lipovova, P. / Duskova, J. / Skalova, T. / Trundova, M. / Kolenko, P. / Fejfarova, K. / Stransky, J. / Svecova, L. / Hasek, J. / Dohnalek, J. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 138.8 KB | Display | ![]() |
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PDB format | ![]() | 105.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 854.2 KB | Display | ![]() |
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Full document | ![]() | 855 KB | Display | |
Data in XML | ![]() | 28 KB | Display | |
Data in CIF | ![]() | 43.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5fb9C ![]() 5fbaC ![]() 5fbbC ![]() 5fbcC ![]() 5fbdC ![]() 5fbfC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: TRP / Beg label comp-ID: TRP / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 21 - 284 / Label seq-ID: 1 - 264
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Components
-Protein / Sugars , 2 types, 6 molecules AB![](data/chem/img/NAG.gif)
![](data/chem/img/NAG.gif)
#1: Protein | Mass: 29082.676 Da / Num. of mol.: 2 / Mutation: D65N Source method: isolated from a genetically manipulated source Details: Mature protein without signal sequence. / Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Sugar | ChemComp-NAG / |
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-Non-polymers , 5 types, 663 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/DCZ.gif)
![](data/chem/img/GNG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/DCZ.gif)
![](data/chem/img/GNG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-GNG / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.64 Å3/Da / Density % sol: 66.2 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.2 M Sodium chloride, 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3,350 Temp details: stable |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 4, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→37.47 Å / Num. obs: 59852 / % possible obs: 99.6 % / Redundancy: 5.8 % / Biso Wilson estimate: 10.4 Å2 / Rmerge(I) obs: 0.131 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 1.97→2.02 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.645 / Mean I/σ(I) obs: 2 / % possible all: 97.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: our previous model of S1 Resolution: 1.97→37.47 Å / Cor.coef. Fo:Fc: 0.963 / SU B: 2.655 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.934 Å2
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Refinement step | Cycle: 1 / Resolution: 1.97→37.47 Å
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Refine LS restraints |
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