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Yorodumi- PDB-5e5e: X-ray structure of the adduct formed in the reaction between RNas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5e5e | ||||||
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Title | X-ray structure of the adduct formed in the reaction between RNase A and a neutral organometallic derivative [Pt(pbi)(Me)(DMSO)], pbi=2-(2'-pyridil)benzimidazole (compound 3) | ||||||
Components | Ribonuclease pancreaticPancreatic ribonuclease family | ||||||
Keywords | HYDROLASE | ||||||
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 / Resolution: 1.98 Å | ||||||
Authors | Merlino, A. | ||||||
Citation | Journal: Dalton Trans / Year: 2015 Title: Cytotoxic properties of a new organometallic platinum(ii) complex and its gold(i) heterobimetallic derivatives. Authors: Serratrice, M. / Maiore, L. / Zucca, A. / Stoccoro, S. / Landini, I. / Mini, E. / Massai, L. / Ferraro, G. / Merlino, A. / Messori, L. / Cinellu, M.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5e5e.cif.gz | 61.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5e5e.ent.gz | 48.2 KB | Display | PDB format |
PDBx/mmJSON format | 5e5e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e5/5e5e ftp://data.pdbj.org/pub/pdb/validation_reports/e5/5e5e | HTTPS FTP |
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-Related 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 | #3: Chemical | ChemComp-DMS / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.48 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.1 Details: RNase A crystals were grown by hanging drop vapor diffusion method using a reservoir solution containing 22-24 % (w/v) PEG4K, 10 mM sodium citrate pH 5.1-5.3. The crystals are monoclinic, ...Details: RNase A crystals were grown by hanging drop vapor diffusion method using a reservoir solution containing 22-24 % (w/v) PEG4K, 10 mM sodium citrate pH 5.1-5.3. The crystals are monoclinic, space group C2, with two molecules in the asymmetric unit. The adduct was prepared by a three-days soaking in a solution that comprised the standard mother liquor used for the crystal growth to which a 2.5 mM solution of compound 3was added PH range: 5.1-5.3 |
-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: Mar 18, 2015 |
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→72.5 Å / Num. obs: 16494 / % possible obs: 98.8 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 4.8 |
Reflection shell | Resolution: 1.98→2.01 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.408 |
-Processing
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Refinement | Resolution: 1.98→72.5 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.924 / SU B: 5.614 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.211 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.33 Å2
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Refinement step | Cycle: 1 / Resolution: 1.98→72.5 Å
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