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Yorodumi- PDB-7p8r: X-ray structure of the adduct of a vanadium picolinate complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7p8r | ||||||
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Title | X-ray structure of the adduct of a vanadium picolinate complex with RNase A at pH 5.1 | ||||||
Components | Ribonuclease pancreatic | ||||||
Keywords | RNA BINDING PROTEIN / vanadium / ribonuclease / metalation | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.27 Å | ||||||
Authors | Ferraro, G. / Merlino, A. | ||||||
Citation | Journal: Inorg.Chem. / Year: 2021 Title: Spectroscopic/Computational Characterization and the X-ray Structure of the Adduct of the V IV O-Picolinato Complex with RNase A. Authors: Ferraro, G. / Demitri, N. / Vitale, L. / Sciortino, G. / Sanna, D. / Ugone, V. / Garribba, E. / Merlino, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7p8r.cif.gz | 125.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7p8r.ent.gz | 95 KB | Display | PDB format |
PDBx/mmJSON format | 7p8r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7p8r_validation.pdf.gz | 857.6 KB | Display | wwPDB validaton report |
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Full document | 7p8r_full_validation.pdf.gz | 859.7 KB | Display | |
Data in XML | 7p8r_validation.xml.gz | 16.6 KB | Display | |
Data in CIF | 7p8r_validation.cif.gz | 25.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p8/7p8r ftp://data.pdbj.org/pub/pdb/validation_reports/p8/7p8r | HTTPS FTP |
-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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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, pancreatic ribonuclease #2: Chemical | ChemComp-AIV / | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.19 Å3/Da / Density % sol: 43.95 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.1 / Details: 22% PEG 4K 10 mM sodium citrate pH 5.1 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.96 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 22, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96 Å / Relative weight: 1 |
Reflection | Resolution: 1.268→72.71 Å / Num. obs: 58090 / % possible obs: 91.3 % / Redundancy: 5 % / CC1/2: 0.992 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.042 / Rrim(I) all: 0.105 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 1.268→1.29 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.664 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2507 / CC1/2: 0.828 / Rpim(I) all: 0.365 / Rrim(I) all: 0.761 / % possible all: 79.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1jvt Resolution: 1.27→72.71 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.958 / SU B: 3.164 / SU ML: 0.054 / Cross valid method: FREE R-VALUE / ESU R: 0.057 / ESU R Free: 0.062 Details: Hydrogens have been added in their 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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.638 Å2
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Refinement step | Cycle: LAST / Resolution: 1.27→72.71 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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