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Yorodumi- PDB-6f60: The x-ray structure of bovine pancreatic ribonuclease in complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6f60 | ||||||
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Title | The x-ray structure of bovine pancreatic ribonuclease in complex with a five-coordinate platinum(II) compound containing a sugar ligand | ||||||
Components | Ribonuclease pancreatic | ||||||
Keywords | HYDROLASE / ribonuclease / platinum(II) compound / five-coordinate / sugar ligand / cytotoxicity | ||||||
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: 1.14 Å | ||||||
Authors | Merlino, A. / Ferraro, G. | ||||||
Citation | Journal: Inorg Chem / Year: 2018 Title: Five-Coordinate Platinum(II) Compounds Containing Sugar Ligands: Synthesis, Characterization, Cytotoxic Activity, and Interaction with Biological Macromolecules. Authors: Cucciolito, M.E. / D'Amora, A. / De Feo, G. / Ferraro, G. / Giorgio, A. / Petruk, G. / Monti, D.M. / Merlino, A. / Ruffo, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6f60.cif.gz | 147.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6f60.ent.gz | 123 KB | Display | PDB format |
PDBx/mmJSON format | 6f60.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6f60_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 6f60_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 6f60_validation.xml.gz | 20.8 KB | Display | |
Data in CIF | 6f60_validation.cif.gz | 31.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f6/6f60 ftp://data.pdbj.org/pub/pdb/validation_reports/f6/6f60 | HTTPS FTP |
-Related structure data
Similar structure data |
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-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
#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-SO4 / | #3: Chemical | ChemComp-DVW / | #4: Chemical | ChemComp-DW5 / | #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: 2.14 Å3/Da / Density % sol: 42.53 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 22% PEG 4K 0.01 M sodium citrate pH 5.1 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Mar 8, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.14→72.34 Å / Num. obs: 80973 / % possible obs: 95.5 % / Redundancy: 2.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.034 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 1.14→1.18 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 0.9 / CC1/2: 0.363 / Rpim(I) all: 0.805 / % possible all: 92.5 |
-Processing
Software |
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Refinement | Resolution: 1.14→72.34 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.971 / SU B: 3.209 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.038 / ESU R Free: 0.044 / 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: 26.744 Å2
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Refinement step | Cycle: 1 / Resolution: 1.14→72.34 Å
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Refine LS restraints |
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