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Open data
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Basic information
Entry | Database: PDB / ID: 4oun | ||||||
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Title | Crystal Structure of Mini-ribonuclease 3 from Bacillus subtilis | ||||||
![]() | Mini-ribonuclease 3 | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Chojnowski, G. / Czarnecka, J. / Nowak, E. / Pianka, D. / Glow, D. / Sabala, I. / Skowronek, K. / Nowotny, M. / Bujnicki, J.M. | ||||||
![]() | ![]() Title: Sequence-specific cleavage of dsRNA by Mini-III RNase Authors: Glow, D. / Pianka, D. / Sulej, A.A. / Kozlowski, L.P. / Czarnecka, J. / Chojnowski, G. / Skowronek, K.J. / Bujnicki, J.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 38.9 KB | Display | ![]() |
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PDB format | ![]() | 26.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1u61S 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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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 18422.740 Da / Num. of mol.: 1 / Mutation: E126Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Strain: 168 / Gene: mrnC, yazC, BSU00950 / Production host: ![]() ![]() ![]() References: UniProt: O31418, ![]() |
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#2: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.55 Å3/Da / Density % sol: 20.43 % |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2M sodium acetate trihydrate, 0.1M TRIS, 30% PEG4000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 24, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→44.7 Å / Num. all: 10956 / Num. obs: 10939 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 36.163 Å2 / Rmerge(I) obs: 0.091 / Χ2: 0.964 / Net I/σ(I): 17.17 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Phasing
Phasing![]() | Method: ![]() | |||||||||
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Phasing MR |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1U61 Resolution: 1.8→44.69 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.938 / SU B: 6.413 / SU ML: 0.176 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R: 0.155 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 95.64 Å2 / Biso mean: 41.917 Å2 / Biso min: 21.79 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→44.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.799→1.846 Å / Total num. of bins used: 20
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