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Open data
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Basic information
Entry | Database: PDB / ID: 1ey7 | ||||||
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Title | STRUCTURE OF S. NUCLEASE STABILIZING MUTANT S128A | ||||||
![]() | STAPHYLOCOCCAL NUCLEASE | ||||||
![]() | HYDROLASE | ||||||
Function / homology | ![]() endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters / micrococcal nuclease / nucleic acid binding / extracellular region / membrane / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Chen, J. / Lu, Z. / Sakon, J. / Stites, W.E. | ||||||
![]() | ![]() Title: Increasing the thermostability of staphylococcal nuclease: implications for the origin of protein thermostability. Authors: Chen, J. / Lu, Z. / Sakon, J. / Stites, W.E. #1: ![]() Title: Contributions of the Polar, Uncharged Amino Acids to the Stability of Staphylococcal Nuclease: Evidence for Mutational Effects on the Free Energy of the Denatured State. Authors: Green, S.M. / Meeker, A.K. / Shortle, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 40.5 KB | Display | ![]() |
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PDB format | ![]() | 28 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1ey0C ![]() 1ey4C ![]() 1ey5C ![]() 1ey6C ![]() 1ey8C ![]() 1ey9C ![]() 1eyaC ![]() 1eycC ![]() 1eydC ![]() 1ez6C ![]() 1ez8C 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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Components
#1: Protein | Mass: 16827.330 Da / Num. of mol.: 1 / Mutation: S128A 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 Å3/Da / Density % sol: 43.56 % | |||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: MPD, Sodium phosphate buffer, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||
Crystal grow | *PLUS Details: MPD, Sodium phosphate buffer, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 297 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | *PLUS Highest resolution: 1.88 Å / Lowest resolution: 6 Å / % possible obs: 94.8 % |
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Processing
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Refinement | Method to determine structure: AB INITIO / Resolution: 1.88→6 Å / Num. parameters: 4660 / Num. restraintsaints: 4488 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 5 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1147 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.88→6 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 7854 / σ(I): 4 / Rfactor obs: 0.1548 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 38.6 Å2 |