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- PDB-5obc: 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: 5obc | ||||||
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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-IM), IM=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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 67.4 KB | Display | ![]() |
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PDB format | ![]() | 48.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 470.3 KB | Display | ![]() |
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Full document | ![]() | 471.4 KB | Display | |
Data in XML | ![]() | 13.6 KB | Display | |
Data in CIF | ![]() | 19.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ob6C ![]() 5ob7C ![]() 5ob8C ![]() 5ob9C ![]() 5obdC ![]() 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
#1: Protein | Mass: 13708.326 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-9Q8 / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.07 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 18% PEG4K, 10 mM sodium citrate pH 5.1 Soaking: 4 days Ligand concen-tration: 5 mM |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Apr 8, 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: 2.07→74.68 Å / Num. obs: 14981 / % possible obs: 99 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 2.07→2.11 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.548 / Mean I/σ(I) obs: 2.5 / % possible all: 94.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1JVT (mol A) Resolution: 2.07→74.68 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.916 / SU B: 6.858 / SU ML: 0.181 / Cross valid method: THROUGHOUT / ESU R: 0.236 / ESU R Free: 0.223 / 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: 42.102 Å2
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Refinement step | Cycle: 1 / Resolution: 2.07→74.68 Å
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Refine LS restraints |
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