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Yorodumi- PDB-1ihz: Structure of S. nuclease mutant quintuple mutant V23L/V66L/I72L/I... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ihz | ||||||
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Title | Structure of S. nuclease mutant quintuple mutant V23L/V66L/I72L/I92L/V99L | ||||||
Components | STAPHYLOCOCCAL NUCLEASEMicrococcal 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 Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / AB INITIO / Resolution: 1.65 Å | ||||||
Authors | Chen, J. / Lu, Z. / Sakon, J. / Stites, W.E. | ||||||
Citation | Journal: Biophys.Chem. / Year: 2004 Title: Proteins with simplified hydrophobic cores compared to other packing mutants. Authors: Chen, J. / Lu, Z. / Sakon, J. / Stites, W.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ihz.cif.gz | 41.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ihz.ent.gz | 29.1 KB | Display | PDB format |
PDBx/mmJSON format | 1ihz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ih/1ihz ftp://data.pdbj.org/pub/pdb/validation_reports/ih/1ihz | HTTPS FTP |
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-Related 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: 16885.410 Da / Num. of mol.: 1 / Mutation: V23L, V66L, I72L, I92L, V99L 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: 2.06 Å3/Da / Density % sol: 40.3 % | |||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: MPD, SODIUM PHOSPHATE BUFFER, pH 8.00, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||
Crystal grow | *PLUS pH: 8 / Method: vapor diffusion, hanging drop / Details: Chen, J., (2000) J.Mol.Biol., 303, 125. | |||||||||||||||
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 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→10 Å / Num. obs: 17142 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 20.7 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO / Resolution: 1.65→8 Å / Num. parameters: 4837 / Num. restraintsaints: 4520 / Cross valid method: FREE R / σ(F): 0 / σ(I): 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: 1165.5 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→8 Å
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Refine LS restraints |
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