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Yorodumi- PDB-6gok: X-ray structure of the adduct formed upon reaction of bovine panc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6gok | ||||||
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Title | X-ray structure of the adduct formed upon reaction of bovine pancreatic ribonuclease with a Pd(II) complex bearing N,N-pyridylbenzimidazole derivative with an alkylated sulphonate side chain | ||||||
Components | Ribonuclease pancreatic | ||||||
Keywords | HYDROLASE / protein-metallodrug interaction / palladium-based drug / N-pyridylbenzimidazole bidentate ligands / stacking / non covalent bond | ||||||
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: 2.65 Å | ||||||
Authors | Merlino, A. / Ferraro, G. | ||||||
Citation | Journal: Dalton Trans / Year: 2018 Title: Exploring the interactions between model proteins and Pd(ii) or Pt(ii) compounds bearing charged N,N-pyridylbenzimidazole bidentate ligands by X-ray crystallography. Authors: Ferraro, G. / Mansour, A.M. / Merlino, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6gok.cif.gz | 63.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gok.ent.gz | 47.1 KB | Display | PDB format |
PDBx/mmJSON format | 6gok.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6gok_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 6gok_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 6gok_validation.xml.gz | 12.8 KB | Display | |
Data in CIF | 6gok_validation.cif.gz | 16.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/go/6gok ftp://data.pdbj.org/pub/pdb/validation_reports/go/6gok | HTTPS FTP |
-Related structure data
Related structure data | 6gobC 6gohC 6goiC 6gojC 1fs3S 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
#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 | #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: 2.18 Å3/Da / Density % sol: 43.57 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.1 / Details: 20% PEG4000 10 mM sodium citrate buffer 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 12, 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: 2.65→72.66 Å / Num. obs: 6649 / % possible obs: 91.1 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 2.65→2.7 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.391 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 286 / CC1/2: 0.834 / % possible all: 79.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1fs3 Resolution: 2.65→72.66 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.889 / SU B: 14.123 / SU ML: 0.286 / Cross valid method: THROUGHOUT / ESU R Free: 0.404 / 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: 48.959 Å2
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Refinement step | Cycle: 1 / Resolution: 2.65→72.66 Å
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Refine LS restraints |
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