+Open data
-Basic information
Entry | Database: PDB / ID: 1a5q | ||||||
---|---|---|---|---|---|---|---|
Title | P93A VARIANT OF BOVINE PANCREATIC RIBONUCLEASE A | ||||||
Components | RIBONUCLEASE APancreatic ribonuclease family | ||||||
Keywords | HYDROLASE / HYDROLASE (NUCLEIC ACID / RNA) | ||||||
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 / DIFFERENCE FOURIER / Resolution: 2.3 Å | ||||||
Authors | Pearson, M.A. / Karplus, P.A. / Dodge, R.W. / Laity, J.H. / Scheraga, H.A. | ||||||
Citation | Journal: Protein Sci. / Year: 1998 Title: Crystal structures of two mutants that have implications for the folding of bovine pancreatic ribonuclease A. Authors: Pearson, M.A. / Karplus, P.A. / Dodge, R.W. / Laity, J.H. / Scheraga, H.A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1a5q.cif.gz | 34.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1a5q.ent.gz | 26.3 KB | Display | PDB format |
PDBx/mmJSON format | 1a5q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a5/1a5q ftp://data.pdbj.org/pub/pdb/validation_reports/a5/1a5q | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 13682.289 Da / Num. of mol.: 1 / Mutation: P93A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Cell line: BL21 / Organ: PANCREAS / Plasmid: PET22B(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P61823, EC: 3.1.27.5 |
---|---|
#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.6 % | ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 6.8 Details: PROTEIN WAS CRYSTALLIZED FROM 100 MM HEPES PH 7.0, 2.2 M CSCL, AND 1.2 M AMM SO4. THEN IT WAS SOAKED IN 100 MM HEPES PH 7.0, 80% AMM SO4 FOR 24 HOURS TO REMOVE THE CS IONS., pH 6.8 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 5.7 / Method: macro seeding | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 298 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: May 8, 1997 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 2.3 Å / Num. obs: 7204 / % possible obs: 97 % / Redundancy: 5 % / Rsym value: 0.134 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 4 / Rsym value: 0.391 / % possible all: 100 |
Reflection | *PLUS Rmerge(I) obs: 0.134 |
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.391 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: DIFFERENCE FOURIER / Resolution: 2.3→10 Å / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→10 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.3→2.4 Å / Total num. of bins used: 10 /
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor obs: 0.288 |