+Open data
-Basic information
Entry | Database: PDB / ID: 5zo4 | ||||||
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Title | inactive state of the nuclease | ||||||
Components | Putative 3'-5' exonuclease family protein | ||||||
Keywords | HYDROLASE / nuclease | ||||||
Function / homology | Function and homology information 3'-5' exonuclease activity / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / nucleic acid binding Similarity search - Function | ||||||
Biological species | Agrobacterium fabrum str. J-07 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å | ||||||
Authors | Yuan, Z.L. / Gu, L.C. | ||||||
Citation | Journal: Front Microbiol / Year: 2018 Title: NrnC, an RNase D-Like Protein FromAgrobacterium, Is a Novel Octameric Nuclease That Specifically Degrades dsDNA but Leaves dsRNA Intact. Authors: Yuan, Z. / Gao, F. / Yin, K. / Gu, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zo4.cif.gz | 93.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zo4.ent.gz | 71.2 KB | Display | PDB format |
PDBx/mmJSON format | 5zo4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5zo4_validation.pdf.gz | 452.4 KB | Display | wwPDB validaton report |
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Full document | 5zo4_full_validation.pdf.gz | 455.1 KB | Display | |
Data in XML | 5zo4_validation.xml.gz | 16.4 KB | Display | |
Data in CIF | 5zo4_validation.cif.gz | 21.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zo/5zo4 ftp://data.pdbj.org/pub/pdb/validation_reports/zo/5zo4 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 23447.658 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrobacterium fabrum str. J-07 (bacteria) Gene: AGR8A_Lc10769 / Production host: Escherichia coli (E. coli) References: UniProt: A0A1S7QSB2, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters #2: Chemical | #3: Chemical | ChemComp-MN / #4: 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: 2.95 Å3/Da / Density % sol: 58.34 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Tris-HCl, pH 8.0, 1 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 13, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 19752 / % possible obs: 100 % / Redundancy: 14.3 % / Net I/σ(I): 60.99 |
Reflection shell | Resolution: 2.5→2.59 Å |
-Processing
Software |
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Refinement | Resolution: 2.5→37.319 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.38 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→37.319 Å
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Refine LS restraints |
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LS refinement shell |
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