[English] 日本語
Yorodumi- PDB-1rny: RIBONUCLEASE A CRYSTALLIZED FROM 3M CESIUM CHLORIDE, 30% AMMONIUM... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rny | ||||||
---|---|---|---|---|---|---|---|
Title | RIBONUCLEASE A CRYSTALLIZED FROM 3M CESIUM 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: 2 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1rny.cif.gz | 38.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1rny.ent.gz | 25.8 KB | Display | PDB format |
PDBx/mmJSON format | 1rny.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1rny_validation.pdf.gz | 360.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1rny_full_validation.pdf.gz | 361.8 KB | Display | |
Data in XML | 1rny_validation.xml.gz | 4.1 KB | Display | |
Data in CIF | 1rny_validation.cif.gz | 6.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rn/1rny ftp://data.pdbj.org/pub/pdb/validation_reports/rn/1rny | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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 | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-CS / | #4: Water | ChemComp-HOH / | Nonpolymer details | CS 200 HAS OCCUPANCY 0.33 | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 5.5 Details: CRYSTALLIZED FROM 80% AMMONIUM SULFATE (PDB ENTRY 1RNO), pH 5.5 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 290 K |
---|---|
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: 2→8.2 Å / Num. obs: 9388 / % possible obs: 84.5 % / Observed criterion σ(I): 1 / Redundancy: 2.34 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 21.91 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: RIBONUCLEASE A Resolution: 2→8 Å / σ(F): 2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.19 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: PROFFT / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.175 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|