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Yorodumi- PDB-8c3b: X-ray structure of RNase A upon reaction with a Ruthenium(II)-are... -
+Open data
-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) | ||||||
Components | Ribonuclease pancreatic | ||||||
Keywords | RNA BINDING PROTEIN / ruthenium / carbene / protein binding | ||||||
Function / homology | Function and homology information 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 | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 Å | ||||||
Authors | Ferraro, G. / Merlino, A. | ||||||
Funding support | 1items
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Citation | Journal: Organometallics / Year: 2023 Title: Ruthenium(II)–Arene Complexes with Glycosylated NHC-Carbene Co-Ligands: Synthesis, Hydrolytic Behavior, and Binding to Biological Molecules Authors: Annunziata, A. / Cucciolito, M.E. / Di Ronza, M. / Ferraro, G. / Hadiji, M. / Merlino, A. / Ortiz, D. / Scopelliti, R. / Fadaei Tirani, F. / Dyson, P.J. / Ruffo, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8c3b.cif.gz | 75.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8c3b.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8c3b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c3/8c3b ftp://data.pdbj.org/pub/pdb/validation_reports/c3/8c3b | HTTPS FTP |
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-Related structure data
Related structure data | 8c39C 1jvtS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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) Bos taurus (cattle) / References: UniProt: P61823, pancreatic ribonuclease |
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-Non-polymers , 5 types, 326 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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