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- PDB-8c3b: X-ray structure of RNase A upon reaction with a Ruthenium(II)-are... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8c3b | ||||||
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Title | X-ray structure of RNase A upon reaction with a Ruthenium(II)-arene Complexed with Glycosylated Carbene Ligands (5) | ||||||
![]() | Ribonuclease pancreatic | ||||||
![]() | RNA BINDING PROTEIN / ruthenium / carbene / protein binding | ||||||
Function / homology | ![]() pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / nucleic acid binding / lyase activity / defense response to Gram-positive bacterium / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ferraro, G. / Merlino, A. | ||||||
Funding support | 1items
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![]() | ![]() Title: Ruthenium(II)-arene Complexes with Glycosylated Carbene Ligands: Synthesis, Characterization, Antiproliferative Activity, In Solution and Crystallographic Evidences of Macromolecule Binding Authors: Annunziata, A. / Cucciolito, M.E. / Di Ronza, M. / Ferraro, G. / Hadiji, M. / Merlino, A. / Scopelliti, R. / Ruffo, F. / Dyson, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 75.5 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 16.3 KB | Display | |
Data in CIF | ![]() | 23.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8c39C ![]() 1jvtS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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
-Protein , 1 types, 2 molecules AAABBB
#1: Protein | Mass: 13708.326 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Non-polymers , 5 types, 326 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/R6U.gif)
![](data/chem/img/T9L.gif)
![](data/chem/img/T9U.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/R6U.gif)
![](data/chem/img/T9L.gif)
![](data/chem/img/T9U.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SO4 / |
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#3: Chemical | ChemComp-R6U / ( |
#4: Chemical | ChemComp-T9L / ( |
#5: Chemical | ChemComp-T9U / ( |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.1 / Details: 22% PEG4k, 10 mM sodium citrate pH 5.1 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 4, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.24→72.63 Å / Num. obs: 59589 / % possible obs: 99.2 % / Redundancy: 6.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.034 / Net I/σ(I): 21.7 |
Reflection shell | Resolution: 1.37→1.39 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.863 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2458 / CC1/2: 0.763 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1jvt Resolution: 1.24→72.63 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.127 / SU ML: 0.047 / Cross valid method: FREE R-VALUE / ESU R: 0.057 / ESU R Free: 0.061 Details: Hydrogens have been added in their 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 BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.745 Å2
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Refinement step | Cycle: LAST / Resolution: 1.24→72.63 Å
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Refine LS restraints |
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LS refinement shell |
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