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Open data
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Basic information
Entry | Database: PDB / ID: 5j21 | ||||||
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Title | Structure of Bacillus NanoRNase A (WT) | ||||||
![]() | Bifunctional oligoribonuclease and PAP phosphatase NrnA | ||||||
![]() | HYDROLASE / nanoRNA / RNA degradation / exonuclease / RNase / B. subtilis / abortive transcripts / pAp phosphatase | ||||||
Function / homology | ![]() 3'(2'),5'-bisphosphate nucleotidase / 3'(2'),5'-bisphosphate nucleotidase activity / exonuclease activity / nucleic acid binding / Hydrolases; Acting on ester bonds Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Schmier, B.J. / Malhotra, A. / Nelersa, C.M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Basis for the Bidirectional Activity of Bacillus nanoRNase NrnA. Authors: Schmier, B.J. / Nelersa, C.M. / Malhotra, A. #1: Journal: Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. Year: 2011 Title: Purification and crystallization of Bacillus subtilis NrnA, a novel enzyme involved in nanoRNA degradation. Authors: Nelersa, C.M. / Schmier, B.J. / Malhotra, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 262.4 KB | Display | ![]() |
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PDB format | ![]() | 211.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 454.7 KB | Display | ![]() |
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Full document | ![]() | 464.5 KB | Display | |
Data in XML | ![]() | 51.2 KB | Display | |
Data in CIF | ![]() | 74.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ippC ![]() 5iufC ![]() 5izoC ![]() 3devS 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: 37483.863 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 168 / Gene: nrnA, ytqI, BSU29250 / Plasmid: pET28a-TEV / Production host: ![]() ![]() References: UniProt: O34600, 3'(2'),5'-bisphosphate nucleotidase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.28 % |
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Crystal grow | Temperature: 298.15 K / Method: vapor diffusion, hanging drop Details: PEG MME 2000, sodium acetate, ammonium acetate, glycerol Temp details: room temperature |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 27, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2→46.44 Å / Num. obs: 93522 / % possible obs: 98.3 % / Redundancy: 5 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 35.19 |
Reflection shell | Resolution: 2→2.03 Å / % possible all: 96.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3DEV Resolution: 2→46.44 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.834 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.167 / ESU R Free: 0.159 / 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: 1.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.44 Å2
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Refinement step | Cycle: LAST / Resolution: 2→46.44 Å
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Refine LS restraints |
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