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Yorodumi- PDB-4s18: The X-ray structure of the adduct formed in the reaction between ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4s18 | ||||||
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Title | The X-ray structure of the adduct formed in the reaction between bovine pancreatic ribonuclease and oxaliplatin | ||||||
Components | Ribonuclease pancreaticPancreatic ribonuclease family | ||||||
Keywords | HYDROLASE / ribonuclease fold / cleavage of RNA / RNA / bovine pancreas | ||||||
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: 2.27 Å | ||||||
Authors | Merlino, A. | ||||||
Citation | Journal: J.Inorg.Biochem. / Year: 2015 Title: Interactions of carboplatin and oxaliplatin with proteins: Insights from X-ray structures and mass spectrometry studies of their ribonuclease A adducts. Authors: Messori, L. / Marzo, T. / Merlino, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4s18.cif.gz | 62.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4s18.ent.gz | 45.7 KB | Display | PDB format |
PDBx/mmJSON format | 4s18.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s1/4s18 ftp://data.pdbj.org/pub/pdb/validation_reports/s1/4s18 | HTTPS FTP |
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-Related structure data
Related structure data | 4s0qC 1jvtS C: citing same article (ref.) S: Starting model for refinement |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 0 / Auth seq-ID: 1 - 124 / Label seq-ID: 1 - 124
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-Components
#1: Protein | Mass: 13708.326 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: RNASE1, RNS1 / References: UniProt: P61823, EC: 3.1.27.5 #2: Chemical | ChemComp-1PT / #3: 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: 2.2 Å3/Da / Density % sol: 44.14 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: RNase A was crystallized at room temperature mixing 1 L solution of protein at 20 mg mL-1 with an equal volume of reservoir solution containing 20% PEG4000 and 20 mM sodium citrate buffer pH ...Details: RNase A was crystallized at room temperature mixing 1 L solution of protein at 20 mg mL-1 with an equal volume of reservoir solution containing 20% PEG4000 and 20 mM sodium citrate buffer pH 5.0. Two weeks after their appearance, single crystals were soaked for four days in a solution of Oxaliplatin dissolved in 10 L of reservoir. At the final, Pt drugs:protein concentrations were in 10:1 ratio, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-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 / Details: mirrors |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.27→50 Å / Num. all: 10764 / Num. obs: 10764 / % possible obs: 95.4 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.161 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb code 1JVT Resolution: 2.27→50 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.862 / SU B: 9.639 / SU ML: 0.233 / Cross valid method: THROUGHOUT / ESU R: 0.465 / ESU R Free: 0.308 / 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: 46.399 Å2
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Refinement step | Cycle: LAST / Resolution: 2.27→50 Å
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Refine LS restraints |
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