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Yorodumi- PDB-5ogh: Structure of RNase A at high resolution (1.16 A) in complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ogh | |||||||||
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Title | Structure of RNase A at high resolution (1.16 A) in complex with 3'-CMP and sulphate ions | |||||||||
Components | Ribonuclease pancreatic | |||||||||
Keywords | HYDROLASE / Ribonuclease A / 3'-CMP / RNase A / mononucleotide inhibitor / high resolution | |||||||||
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: 1.16 Å | |||||||||
Authors | Blanco, J.A. / Prats-Ejarque, G. / Salazar, V.A. / Moussaoui, M. / Boix, E. | |||||||||
Funding support | Spain, 2items
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Citation | Journal: Biochim Biophys Acta Gen Subj / Year: 2019 Title: Characterization of an RNase with two catalytic centers. Human RNase6 catalytic and phosphate-binding site arrangement favors the endonuclease cleavage of polymeric substrates. Authors: Prats-Ejarque, G. / Blanco, J.A. / Salazar, V.A. / Nogues, V.M. / Moussaoui, M. / Boix, E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ogh.cif.gz | 103.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ogh.ent.gz | 80.1 KB | Display | PDB format |
PDBx/mmJSON format | 5ogh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ogh_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5ogh_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5ogh_validation.xml.gz | 10.1 KB | Display | |
Data in CIF | 5ogh_validation.cif.gz | 14.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/og/5ogh ftp://data.pdbj.org/pub/pdb/validation_reports/og/5ogh | HTTPS FTP |
-Related structure data
Related structure data | 5et4C 5oabC 6enpC 1kf3S 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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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 13708.326 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: Pancreas / Tissue: Pancreatic / References: UniProt: P61823, EC: 3.1.27.5 |
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-Non-polymers , 5 types, 189 molecules
#2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: Chemical | ChemComp-CL / #5: Chemical | #6: 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: 2.78 Å3/Da / Density % sol: 55.76 % / Description: Hexagonal |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.54 M ammonium sulphate, 1.25 M sodium chloride, 0.1 M sodium acetate pH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 14, 2014 Details: VERTICAL FOCUSING MIRROR (VFM) AND A HORIZONTAL FOCUSING MIRROR (HFM), MANUFACTURED BY IRELEC |
Radiation | Monochromator: CHANNEL-CUT DOUBLE CRYSTAL MONOCHROMATOR (CINEL), CRYOCOOLED, 6MM GAP Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.16→28.65 Å / Num. obs: 52994 / % possible obs: 100 % / Redundancy: 10.65 % / Biso Wilson estimate: 14.4 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 20.9 |
Reflection shell | Resolution: 1.16→1.22 Å / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 3.6 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1KF3 Resolution: 1.16→28.648 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 10.73
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.13 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.16→28.648 Å
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Refine LS restraints |
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LS refinement shell |
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