[English] 日本語
Yorodumi- PDB-1loy: X-ray structure of the H40A/E58A mutant of Ribonuclease T1 comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1loy | ||||||
---|---|---|---|---|---|---|---|
Title | X-ray structure of the H40A/E58A mutant of Ribonuclease T1 complexed with 3'-guanosine monophosphate | ||||||
Components | Guanyl-specific ribonuclease T1 | ||||||
Keywords | HYDROLASE / RNase / catalytic dyad / nucleophile activation / ab initio calculations | ||||||
Function / homology | Function and homology information hyphal tip / ribonuclease T1 activity / ribonuclease T1 / cell septum / RNA endonuclease activity / lyase activity / RNA binding Similarity search - Function | ||||||
Biological species | Aspergillus oryzae (mold) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Mignon, P. / Steyaert, J. / Loris, R. / Geerlings, P. / Loverix, S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: A nucleophile activation dyad in ribonucleases. A combined X-ray crystallographic/ab initio quantum chemical study Authors: Mignon, P. / Steyaert, J. / Loris, R. / Geerlings, P. / Loverix, S. | ||||||
History |
| ||||||
Remark 999 | The isozyme of RNase T1 used here contains a lysine at position 25. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1loy.cif.gz | 35.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1loy.ent.gz | 22.3 KB | Display | PDB format |
PDBx/mmJSON format | 1loy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lo/1loy ftp://data.pdbj.org/pub/pdb/validation_reports/lo/1loy | HTTPS FTP |
---|
-Related structure data
Related structure data | 1lovC 1lowC 1rgaS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 10969.589 Da / Num. of mol.: 1 / Mutation: H40A/E58A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus oryzae (mold) / Plasmid: pMC / Production host: Escherichia coli (E. coli) / Strain (production host): WK6 / References: UniProt: P00651, EC: 3.1.27.3 |
---|---|
#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-3GP / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 39.92 % | ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2 Details: MPD,CaCl2,sodium acetate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7.2 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 293 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 30, 2000 |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→33.4 Å / Num. all: 12848 / Num. obs: 12848 / % possible obs: 94.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 18.9 Å2 / Rmerge(I) obs: 0.059 |
Reflection shell | Resolution: 1.55→1.61 Å / Rmerge(I) obs: 0.457 / % possible all: 89.9 |
Reflection | *PLUS % possible obs: 94.48 % |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RGA Resolution: 1.55→33.4 Å / Cross valid method: THROUGHOUT / σ(F): 0.001 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→33.4 Å
| ||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
|