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- PDB-5obd: X-ray structure of the adduct formed upon reaction of ribonucleas... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5obd | ||||||
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Title | X-ray structure of the adduct formed upon reaction of ribonuclease A with the compound fac-[RuII(CO)3Cl2(N3-MIM), MIM=methyl-imidazole | ||||||
![]() | Ribonuclease pancreatic | ||||||
![]() | HYDROLASE / protein-metallodrug interaction / CO releasing molecules | ||||||
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 | ![]() ![]() | ||||||
![]() | Pontillo, N. / Ferraro, G. / Merlino, A. | ||||||
![]() | ![]() Title: Ru-Based CO releasing molecules with azole ligands: interaction with proteins and the CO release mechanism disclosed by X-ray crystallography. Authors: Pontillo, N. / Ferraro, G. / Messori, L. / Tamasi, G. / Merlino, 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 | ![]() | 72.3 KB | Display | ![]() |
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PDB format | ![]() | 53.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 461.3 KB | Display | ![]() |
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Full document | ![]() | 462.8 KB | Display | |
Data in XML | ![]() | 16.1 KB | Display | |
Data in CIF | ![]() | 24.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ob6C ![]() 5ob7C ![]() 5ob8C ![]() 5ob9C ![]() 5obcC ![]() 5obeC ![]() 1jvtS 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 13708.326 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.82 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 22% PEG4K, 10 mM sodium cit-rate pH 5.1 Soaking: 14 days Ligand concentration: 5 mM |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: May 28, 2014 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→72.25 Å / Num. obs: 15576 / % possible obs: 92.2 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 1.98→2.1 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 2.2 / % possible all: 81.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1JVT mol A Resolution: 1.98→72.25 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.875 / SU B: 6.113 / SU ML: 0.168 / Cross valid method: THROUGHOUT / ESU R: 0.245 / ESU R Free: 0.231 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.535 Å2
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Refinement step | Cycle: 1 / Resolution: 1.98→72.25 Å
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Refine LS restraints |
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