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- PDB-4rsk: STRUCTURE OF THE K7A/R10A/K66A VARIANT OF RIBONUCLEASE A COMPLEXE... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4rsk | ||||||
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Title | STRUCTURE OF THE K7A/R10A/K66A VARIANT OF RIBONUCLEASE A COMPLEXED WITH 3'-UMP | ||||||
![]() | RIBONUCLEASE A | ||||||
![]() | HYDROLASE / ENDONUCLEASE / RIBONUCLEASE A / SITE-DIRECTED MUTAGENESIS | ||||||
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 | ![]() | ||||||
![]() | Schultz, L.W. / Fisher, B.M. / Raines, R.T. | ||||||
![]() | ![]() Title: Coulombic Effects of Remote Subsites on the Active Site of Ribonuclease A Authors: Fisher, B.M. / Schultz, L.W. / Raines, R.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 | ![]() | 35 KB | Display | ![]() |
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PDB format | ![]() | 26.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438.8 KB | Display | ![]() |
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Full document | ![]() | 437.9 KB | Display | |
Data in XML | ![]() | 4.2 KB | Display | |
Data in CIF | ![]() | 6.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3rskSC S: Starting model for refinement 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 13506.006 Da / Num. of mol.: 1 / Mutation: K7A, R10A, K66A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-U3P / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.47 Å3/Da / Density % sol: 60 % | ||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 4.5 Details: CRYSTALS WERE PREPARED USING THE HANGING DROP METHOD. LYOPHILIZED K7A/R10A/K66A RNASE A WAS DISSOLVED IN UNBUFFERED WATER TO A CONCENTRATION OF 60MG/ML. DROPS CONSISTING OF PROTEIN SOLUTION ...Details: CRYSTALS WERE PREPARED USING THE HANGING DROP METHOD. LYOPHILIZED K7A/R10A/K66A RNASE A WAS DISSOLVED IN UNBUFFERED WATER TO A CONCENTRATION OF 60MG/ML. DROPS CONSISTING OF PROTEIN SOLUTION (1.5MICROLITER), WATER (1.5MICROLITER), AND RESERVOIR SOLUTION (3.0MICROLITER) WERE SUSPENDED OVER 0.5 ML OF RESERVOIR SOLUTION (0.1M SODIUM ACETATE BUFFER, PH 4.5, CONTAINING 36% PEG 4000). THE COMPLEX WITH 3'-UMP WAS PREPARED BY SOAKING CRYSTALS IN MOTHER LIQUOR CONTAINING 5MM 3'-UMP FOR 2 DAYS., vapor diffusion - hanging drop | ||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 273 K |
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Diffraction source | Source: ![]() |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Sep 12, 1997 / Details: LONG MIRRORS |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. obs: 33552 / % possible obs: 88 % / Observed criterion σ(I): 0.33 / Redundancy: 2.4 % / Rsym value: 0.026 / Net I/σ(I): 19.8 |
Reflection shell | Resolution: 2.1→2.2 Å / Rsym value: 0.12 / % possible all: 88 |
Reflection | *PLUS Num. obs: 14210 / Num. measured all: 33552 / Rmerge(I) obs: 0.026 |
Reflection shell | *PLUS % possible obs: 88 % / Rmerge(I) obs: 0.122 |
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Processing
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Refinement | Method to determine structure: DIFFERENCE FOURIER Starting model: PDB ENTRY 3RSK Resolution: 2.1→30 Å / Isotropic thermal model: TNT BCORREL / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
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Solvent computation | Solvent model: BABINET SCALING / Bsol: 135 Å2 / ksol: 0.56 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→30 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5E / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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