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Yorodumi- PDB-5obe: X-ray structure of the adduct formed upon reaction of ribonucleas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5obe | ||||||
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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-MBI), MBI=methyl-benzimidazole | ||||||
Components | Ribonuclease pancreaticPancreatic ribonuclease family | ||||||
Keywords | HYDROLASE / protein-metallodrug interaction / CO releasing molecules | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.82 Å | ||||||
Authors | Pontillo, N. / Ferraro, G. / Merlino, A. | ||||||
Citation | Journal: Dalton Trans / Year: 2017 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5obe.cif.gz | 74.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5obe.ent.gz | 54.6 KB | Display | PDB format |
PDBx/mmJSON format | 5obe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ob/5obe ftp://data.pdbj.org/pub/pdb/validation_reports/ob/5obe | HTTPS FTP |
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-Related structure data
Related structure data | 5ob6C 5ob7C 5ob8C 5ob9C 5obcC 5obdC 1jvtS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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) Bos taurus (cattle) / References: UniProt: P61823, EC: 3.1.27.5 #2: Chemical | ChemComp-RU2 / | #3: Chemical | #4: Chemical | ChemComp-9Q8 / | #5: Water | ChemComp-HOH / | |
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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: 2.21 Å3/Da / Density % sol: 44.37 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 22% PEG4K, 10 mM sodium citrate pH 5.1 Soaking: 3 days Ligand con-centration: 5 mM |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Oct 6, 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: 1.82→73.05 Å / Num. obs: 21285 / % possible obs: 97.6 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 6.3 |
Reflection shell | Resolution: 1.82→1.85 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.384 / Mean I/σ(I) obs: 1.7 / % possible all: 95.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1JVT mol A Resolution: 1.82→73.05 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.936 / SU B: 4.253 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.149 / ESU R Free: 0.153 / 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: 30.82 Å2
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Refinement step | Cycle: 1 / Resolution: 1.82→73.05 Å
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Refine LS restraints |
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