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Yorodumi- PDB-6qe9: The X-ray structure of the adduct formed in the reaction between ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6qe9 | ||||||
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Title | The X-ray structure of the adduct formed in the reaction between bovine pancreatic ribonuclease and complex I, a pentacoordinate Pt(II) compound containing 2,9-dimethyl-1,10-phenanthroline, dimethylfumarate, methyl and iodine as ligands | ||||||
Components | Ribonuclease pancreaticPancreatic ribonuclease family | ||||||
Keywords | HYDROLASE / five-coordinate Pt complexes / anticancer platinum compounds / protein metal coordination | ||||||
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: 2.03 Å | ||||||
Authors | Merlino, A. / Ferraro, G. | ||||||
Citation | Journal: Int J Mol Sci / Year: 2019 Title: Reaction with Proteins of a Five-Coordinate Platinum(II) Compound. Authors: Ferraro, G. / Marzo, T. / Cucciolito, M.E. / Ruffo, F. / Messori, L. / Merlino, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qe9.cif.gz | 65.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qe9.ent.gz | 48.2 KB | Display | PDB format |
PDBx/mmJSON format | 6qe9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qe/6qe9 ftp://data.pdbj.org/pub/pdb/validation_reports/qe/6qe9 | HTTPS FTP |
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-Related structure data
Related structure data | 6qeaC 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-SO4 / | #3: Chemical | #4: 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: 1.9 Å3/Da / Density % sol: 35.2 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.1 / Details: 22% PEG4K 0.01 M sodium citrate pH 5.1 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Jan 17, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→50 Å / Num. obs: 12949 / % possible obs: 94.8 % / Redundancy: 2.8 % / Biso Wilson estimate: 30.08 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 2.03→2.07 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.528 / Mean I/σ(I) obs: 2.3 / % possible all: 92.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1JVT Resolution: 2.03→22.89 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.925 / SU B: 5.811 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.27 / ESU R Free: 0.22 / 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: 30.826 Å2
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Refinement step | Cycle: LAST / Resolution: 2.03→22.89 Å
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Refine LS restraints |
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