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- PDB-3d5g: Structure of ribonuclease Sa2 complexes with mononucleotides: new... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3d5g | ||||||
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Title | Structure of ribonuclease Sa2 complexes with mononucleotides: new aspects of catalytic reaction and substrate recognition | ||||||
![]() | Ribonuclease | ||||||
![]() | HYDROLASE / ribonuclease | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bauerova-Hlinkova, V. / Dvorsky, R. / Povazanec, F. / Sevcik, J. | ||||||
![]() | ![]() Title: Structure of RNase Sa2 complexes with mononucleotides - new aspects of catalytic reaction and substrate recognition Authors: Bauerova-Hlinkova, V. / Dvorsky, R. / Perecko, D. / Povazanec, F. / Sevcik, 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 | ![]() | 147.7 KB | Display | ![]() |
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PDB format | ![]() | 117.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 455.7 KB | Display | ![]() |
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Full document | ![]() | 462.3 KB | Display | |
Data in XML | ![]() | 20.5 KB | Display | |
Data in CIF | ![]() | 30.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3d4aC ![]() 3d5iC ![]() 3dgyC ![]() 3dh2C ![]() 1pylS S: Starting model for refinement 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 10909.012 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58.14 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 30% ammonium sulphate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 15, 2000 |
Radiation | Monochromator: monochromator SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→12 Å / Num. all: 34199 / Num. obs: 34199 / % possible obs: 97.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Biso Wilson estimate: 24.34 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 32.16 |
Reflection shell | Resolution: 1.8→1.82 Å / Rmerge(I) obs: 0.24 / % possible all: 74.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1PYL Resolution: 1.8→11.98 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.92 / SU B: 5.78 / SU ML: 0.083 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.203 / ESU R Free: 0.132 / 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: 22.318 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→11.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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