+Open data
-Basic information
Entry | Database: PDB / ID: 1ey7 | ||||||
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Title | STRUCTURE OF S. NUCLEASE STABILIZING MUTANT S128A | ||||||
Components | STAPHYLOCOCCAL NUCLEASE | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information 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 | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / AB INITIO / Resolution: 1.88 Å | ||||||
Authors | Chen, J. / Lu, Z. / Sakon, J. / Stites, W.E. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 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: Journal: Biochemistry / Year: 1992 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ey7.cif.gz | 40.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ey7.ent.gz | 28 KB | Display | PDB format |
PDBx/mmJSON format | 1ey7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ey7_validation.pdf.gz | 364.6 KB | Display | wwPDB validaton report |
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Full document | 1ey7_full_validation.pdf.gz | 369.9 KB | Display | |
Data in XML | 1ey7_validation.xml.gz | 4.7 KB | Display | |
Data in CIF | 1ey7_validation.cif.gz | 6.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ey/1ey7 ftp://data.pdbj.org/pub/pdb/validation_reports/ey/1ey7 | HTTPS FTP |
-Related structure data
Related structure data | 1ey0C 1ey4C 1ey5C 1ey6C 1ey8C 1ey9C 1eyaC 1eycC 1eydC 1ez6C 1ez8C C: citing same article (ref.) |
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Similar structure data |
-Links
-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.) Staphylococcus aureus (bacteria) / Strain: FOGGI / Production host: Escherichia coli (E. coli) / References: UniProt: P00644, micrococcal nuclease |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
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 % |
-Processing
Software |
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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 |