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Yorodumi- PDB-8r5v: Crystal structure of bovine pancreatic ribonuclease A in complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8r5v | ||||||
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Title | Crystal structure of bovine pancreatic ribonuclease A in complex with [Sp-PS]-mU-dT dinucleotide | ||||||
Components | Ribonuclease pancreatic | ||||||
Keywords | HYDROLASE / complex / dinucleotide / inhibitor / ribonuclease / RNase | ||||||
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: 1.8 Å | ||||||
Authors | Dolot, R. / Jastrzebska, K. / Antonczyk, P. | ||||||
Funding support | Poland, 1items
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Citation | Journal: To Be Published Title: Synthesis of P-stereodefined morpholino dinucleoside-3',6'-thiophosphoramidates using unexpected activator. Authors: Jastrzebska, K. / Antonczyk, P. / Dolot, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8r5v.cif.gz | 79 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8r5v.ent.gz | 54.1 KB | Display | PDB format |
PDBx/mmJSON format | 8r5v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r5/8r5v ftp://data.pdbj.org/pub/pdb/validation_reports/r5/8r5v | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 16480.896 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: pancreas / References: UniProt: P61823 #2: Chemical | ChemComp-Y4I / | #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: 2.14 Å3/Da / Density % sol: 42.57 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 22-25 % (w/v) PEG 4000, 20 mM sodium citrate pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SEALED TUBE / Type: RIGAKU PhotonJet-S / Wavelength: 1.54184 Å |
Detector | Type: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Jul 14, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54184 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→17.435 Å / Num. obs: 22015 / % possible obs: 98.8 % / Redundancy: 3.1 % / Biso Wilson estimate: 9.4 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.051 / Rrim(I) all: 0.094 / Χ2: 0.91 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 1.8→1.84 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.243 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 1248 / CC1/2: 0.93 / Rpim(I) all: 0.161 / Rrim(I) all: 0.294 / Χ2: 0.68 / % possible all: 95.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→17.435 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.92 / WRfactor Rfree: 0.22 / WRfactor Rwork: 0.154 / SU B: 3.168 / SU ML: 0.098 / Average fsc free: 0.9629 / Average fsc work: 0.9811 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.144 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: 15.904 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→17.435 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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