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Yorodumi- PDB-7r1p: X-ray structure of the adduct formed upon reaction of the gold(I)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7r1p | ||||||
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Title | X-ray structure of the adduct formed upon reaction of the gold(I) N-heterocyclic carbene complex Au1 with RNase A | ||||||
Components | Ribonuclease pancreatic | ||||||
Keywords | RNA BINDING PROTEIN / metallodrug / protein-metal interaction / gold / carbene / anticancer | ||||||
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: 1.42 Å | ||||||
Authors | Merlino, A. / Ferraro, G. | ||||||
Funding support | 1items
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Citation | Journal: Dalton Trans / Year: 2022 Title: Halo complexes of gold(I) containing glycoconjugate carbene ligands: synthesis, characterization, cytotoxicity and interaction with proteins and DNA model systems. Authors: Annunziata, A. / Ferraro, G. / Cucciolito, M.E. / Imbimbo, P. / Tuzi, A. / Monti, D.M. / Merlino, A. / Ruffo, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7r1p.cif.gz | 71.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7r1p.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7r1p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7r1p_validation.pdf.gz | 904.8 KB | Display | wwPDB validaton report |
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Full document | 7r1p_full_validation.pdf.gz | 906.4 KB | Display | |
Data in XML | 7r1p_validation.xml.gz | 14.4 KB | Display | |
Data in CIF | 7r1p_validation.cif.gz | 20.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r1/7r1p ftp://data.pdbj.org/pub/pdb/validation_reports/r1/7r1p | HTTPS FTP |
-Related structure data
Related structure data | 7r1qC 1jvtS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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, pancreatic ribonuclease #2: Chemical | #3: Chemical | ChemComp-SO4 / | #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: 2.18 Å3/Da / Density % sol: 43.71 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.1 / Details: 22% PEG4K 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: Jul 27, 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: 1.42→50.36 Å / Num. obs: 43467 / % possible obs: 96.1 % / Redundancy: 6.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.031 / Rrim(I) all: 0.08 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 1.42→1.45 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.599 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 2063 / CC1/2: 0.807 / Rpim(I) all: 0.248 / Rrim(I) all: 0.661 / % possible all: 94.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1JVT Resolution: 1.42→50.36 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.309 / SU ML: 0.052 / Cross valid method: FREE R-VALUE / ESU R: 0.073 / ESU R Free: 0.075 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: 23.39 Å2
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Refinement step | Cycle: LAST / Resolution: 1.42→50.36 Å
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Refine LS restraints |
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LS refinement shell |
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