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Yorodumi- PDB-1rnx: RIBONUCLEASE A CRYSTALLIZED FROM 3M SODIUM CHLORIDE, 30% AMMONIUM... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rnx | ||||||
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Title | RIBONUCLEASE A CRYSTALLIZED FROM 3M SODIUM CHLORIDE, 30% AMMONIUM SULFATE | ||||||
Components | RIBONUCLEASE A | ||||||
Keywords | HYDROLASE (PHOSPHORIC DIESTER) / HYDROLASE / RIBONUCLEASE / PHOSPHORIC DIESTER | ||||||
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: 1.9 Å | ||||||
Authors | Fedorov, A.A. / Joseph-Mccarthy, D. / Fedorov, L. / Sirakova, D. / Graf, I. / Almo, S.C. | ||||||
Citation | Journal: Biochemistry / Year: 1996 Title: Ionic interactions in crystalline bovine pancreatic ribonuclease A. Authors: Fedorov, A.A. / Joseph-McCarthy, D. / Fedorov, E. / Sirakova, D. / Graf, I. / Almo, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rnx.cif.gz | 37.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rnx.ent.gz | 25.4 KB | Display | PDB format |
PDBx/mmJSON format | 1rnx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1rnx_validation.pdf.gz | 365.9 KB | Display | wwPDB validaton report |
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Full document | 1rnx_full_validation.pdf.gz | 366.9 KB | Display | |
Data in XML | 1rnx_validation.xml.gz | 4 KB | Display | |
Data in CIF | 1rnx_validation.cif.gz | 6.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rn/1rnx ftp://data.pdbj.org/pub/pdb/validation_reports/rn/1rnx | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 13708.326 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: PANCREAS / References: UniProt: P61823, EC: 3.1.27.5 | ||
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#2: Chemical | ChemComp-CL / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57 % | ||||||||||||||||||||||||
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Crystal grow | pH: 5.5 Details: CRYSTALLIZED FROM 80% AMMONIUM SULFATE (PDB ENTRY 1RNO), pH 5.5 | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: batch method | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 290 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: SIEMENS-NICOLET X100 / Detector: AREA DETECTOR / Date: 1993 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→17.2 Å / Num. obs: 10518 / % possible obs: 82.7 % / Observed criterion σ(I): 1 / Redundancy: 2.92 % / Rmerge(I) obs: 0.035 / Net I/σ(I): 23.68 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: RIBONUCLEASE A Resolution: 1.9→8 Å / σ(F): 2
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Displacement parameters | Biso mean: 19.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.19 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→8 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Name: PROFFT / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.162 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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