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Yorodumi- PDB-5fbc: S1 nuclease from Aspergillus oryzae in complex with 2'-deoxyadeno... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fbc | ||||||||||||
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Title | S1 nuclease from Aspergillus oryzae in complex with 2'-deoxyadenosine-5'-thio-monophosphate (5'dAMP(S)). | ||||||||||||
Components | Nuclease S1 | ||||||||||||
Keywords | HYDROLASE / Endonuclease / Zinc dependent / Complex | ||||||||||||
Function / homology | Function and homology information Aspergillus nuclease S1 / nuclease activity / DNA catabolic process / endonuclease activity / nucleic acid binding / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Aspergillus oryzae RIB40 (mold) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||||||||
Authors | Koval, T. / Oestergaard, L.H. / Dohnalek, J. | ||||||||||||
Funding support | Czech Republic, 3items
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Citation | Journal: PLoS ONE / Year: 2016 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fbc.cif.gz | 78.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fbc.ent.gz | 55 KB | Display | PDB format |
PDBx/mmJSON format | 5fbc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fbc_validation.pdf.gz | 817.2 KB | Display | wwPDB validaton report |
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Full document | 5fbc_full_validation.pdf.gz | 819.5 KB | Display | |
Data in XML | 5fbc_validation.xml.gz | 15.1 KB | Display | |
Data in CIF | 5fbc_validation.cif.gz | 22.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fb/5fbc ftp://data.pdbj.org/pub/pdb/validation_reports/fb/5fbc | HTTPS FTP |
-Related structure data
Related structure data | 5fb9C 5fbaC 5fbbC 5fbdC 5fbfC 5fbgC 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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Unit cell |
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-Components
-Protein / Sugars , 2 types, 3 molecules A
#1: Protein | Mass: 29083.660 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Mature protein without signal sequence. / Source: (gene. exp.) Aspergillus oryzae RIB40 (mold) / Gene: nucS, AO090001000075 / Production host: Aspergillus oryzae (mold) / References: UniProt: P24021, Aspergillus nuclease S1 |
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#3: Sugar |
-Non-polymers , 4 types, 273 molecules
#2: Chemical | #4: Chemical | ChemComp-AS / | #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.1 % |
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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: SYNCHROTRON / Site: BESSY / Beamline: 14.3 / Wavelength: 0.8945 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 16, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8945 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→46.14 Å / Num. obs: 24085 / % possible obs: 99.8 % / Redundancy: 3.5 % / Biso Wilson estimate: 11.1 Å2 / Rmerge(I) obs: 0.101 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 1.75→1.78 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.663 / Mean I/σ(I) obs: 2 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: our previous model of S1 Resolution: 1.75→46.14 Å / Cor.coef. Fo:Fc: 0.972 / SU B: 1.881 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.097 / 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: 15.053 Å2
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Refinement step | Cycle: 1 / Resolution: 1.75→46.14 Å
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