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Yorodumi- PDB-4ot4: X-ray Structure of the Adduct formed between cisplatin and Ribonu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ot4 | ||||||
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Title | X-ray Structure of the Adduct formed between cisplatin and Ribonuclease A | ||||||
Components | Ribonuclease pancreaticPancreatic ribonuclease family | ||||||
Keywords | HYDROLASE / RNase A fold | ||||||
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: 1.85 Å | ||||||
Authors | Messori, L. / Merlino, A. | ||||||
Citation | Journal: Inorg.Chem. / Year: 2014 Title: Cisplatin binding to proteins: molecular structure of the ribonuclease a adduct. Authors: 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 | 4ot4.cif.gz | 62.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ot4.ent.gz | 46.4 KB | Display | PDB format |
PDBx/mmJSON format | 4ot4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ot/4ot4 ftp://data.pdbj.org/pub/pdb/validation_reports/ot/4ot4 | HTTPS FTP |
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-Related structure data
Related structure data | 1jvtS 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
#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 | #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: 1.99 Å3/Da / Density % sol: 38.28 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: Crystals of RNase A were grown by hanging-drop vapor diffusion technique at 298 K mixing a protein solution containing 20 mg mL-1 of RNase A with equal volumes of reservoir solution. Well ...Details: Crystals of RNase A were grown by hanging-drop vapor diffusion technique at 298 K mixing a protein solution containing 20 mg mL-1 of RNase A with equal volumes of reservoir solution. Well diffracting crystals appeared within 15days from the following conditions:20% PEG4000 and 20 mM sodium citrate buffer pH 5.0. , VAPOR DIFFUSION, HANGING DROP |
-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 |
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: 1.85→50 Å / Num. all: 17075 / Num. obs: 17075 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB code 1JVT Resolution: 1.85→30.88 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.915 / SU B: 3.675 / SU ML: 0.112 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.188 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: PHI/PSI TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN PLOT ARE ASSOCIATED WITH RESIDUES THAT ARE NOT WELL DEFINED IN THE ELECTRON DENSITY MAPS (RESIDUES 16-22 OF THE TWO CHAINS AND ...Details: PHI/PSI TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN PLOT ARE ASSOCIATED WITH RESIDUES THAT ARE NOT WELL DEFINED IN THE ELECTRON DENSITY MAPS (RESIDUES 16-22 OF THE TWO CHAINS AND RESIDUES IN CLOSE CONTACT WITH THESE REGIONS).
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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: 27.794 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→30.88 Å
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