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Open data
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Basic information
Entry | Database: PDB / ID: 4rsd | ||||||
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Title | STRUCTURE OF THE D121A VARIANT OF RIBONUCLEASE A | ||||||
![]() | 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. / Quirk, D.J. / Raines, R.T. | ||||||
![]() | ![]() Title: His...Asp catalytic dyad of ribonuclease A: structure and function of the wild-type, D121N, and D121A enzymes. Authors: Schultz, L.W. / Quirk, D.J. / 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 | ![]() | 34.9 KB | Display | ![]() |
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PDB format | ![]() | 26.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 383.1 KB | Display | ![]() |
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Full document | ![]() | 384.9 KB | Display | |
Data in XML | ![]() | 4.4 KB | Display | |
Data in CIF | ![]() | 6.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3rsdC ![]() 1rphS 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
#1: Protein | Mass: 13664.316 Da / Num. of mol.: 1 / Mutation: D121A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-ACT / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 60 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.3 Details: DROPS CONSISTING OF 1.5UL OF A 60MG/ML PROTEIN SOLUTION, 1.5UL OF H2O AND 3UL OF RESERVOIR SOLUTION WERE SUSPENDED OVER A 0.5ML RESERVOIR CONTAINING A SOLUTION OF 2.5M NAOAC, PH 5.3 IN ...Details: DROPS CONSISTING OF 1.5UL OF A 60MG/ML PROTEIN SOLUTION, 1.5UL OF H2O AND 3UL OF RESERVOIR SOLUTION WERE SUSPENDED OVER A 0.5ML RESERVOIR CONTAINING A SOLUTION OF 2.5M NAOAC, PH 5.3 IN SATURATING NACL. TEMP. 20C. | |||||||||||||||||||||||||||||||||||
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: 277 K |
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Diffraction source | Source: ![]() |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Feb 7, 1996 / 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: 1.6→30 Å / Num. obs: 27087 / % possible obs: 91 % / Observed criterion σ(I): 0.33 / Redundancy: 2.1 % / Rsym value: 0.029 / Net I/σ(I): 20 |
Reflection shell | Resolution: 1.6→1.7 Å / Rmerge(I) obs: 0.14 / % possible all: 85 |
Reflection | *PLUS Num. measured all: 56287 / Rmerge(I) obs: 0.029 |
Reflection shell | *PLUS Rmerge(I) obs: 0.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1RPH Resolution: 1.6→30 Å / Isotropic thermal model: TNT BCORREL / σ(F): 0 / Stereochemistry target values: TNT PROTGEO / Details: ASP 83 IS MODELED WITH TWO DIFFERENT POSITIONS.
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Solvent computation | Solvent model: BABINET SCALING / Bsol: 164 Å2 / ksol: 0.79 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→30 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5E / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor all: 0.18 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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