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Open data
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Basic information
Entry | Database: PDB / ID: 1izp | ||||||
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Title | F46L mutant of bovine pancreatic ribonuclease A | ||||||
![]() | RIBONUCLEASE A | ||||||
![]() | HYDROLASE / RIBONUCLEASE / RNASE A / BOVINE PANCREAS | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Kadonosono, T. / Chatani, E. / Hayashi, R. / Moriyama, H. / Ueki, T. | ||||||
![]() | ![]() Title: Minimization of cavity size ensures protein stability and folding: structures of Phe46-replaced bovine pancreatic RNase A Authors: Kadonosono, T. / Chatani, E. / Hayashi, R. / Moriyama, H. / Ueki, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 40.6 KB | Display | ![]() |
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PDB format | ![]() | 27.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 428.6 KB | Display | ![]() |
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Full document | ![]() | 432.2 KB | Display | |
Data in XML | ![]() | 9.5 KB | Display | |
Data in CIF | ![]() | 13.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1izqC ![]() 1izrC ![]() 1izs ![]() 1izt ![]() 1izu ![]() 1izv ![]() 1izw ![]() 1izx C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Details | The biological assembly is a monomer |
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Components
#1: Protein | Mass: 13674.311 Da / Num. of mol.: 1 / Mutation: F46L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.61 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: ammonium sulfate, sodium chloride, sodium acetate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 25 ℃ / pH: 8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 12, 2000 |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 24330 / % possible obs: 99.2 % / Observed criterion σ(I): 1 / Redundancy: 9 % / Biso Wilson estimate: 12.4 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 9 % / Rmerge(I) obs: 0.191 / % possible all: 99.6 |
Reflection | *PLUS Highest resolution: 1.5 Å / Num. obs: 24356 / Rmerge(I) obs: 0.05 |
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Processing
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Refinement | Resolution: 1.5→6 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 696851.51 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 117.628 Å2 / ksol: 0.866345 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 15.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.5→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.59 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Rfactor Rfree: 0.23 / Rfactor Rwork: 0.2 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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