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Yorodumi- PDB-4l2d: X-ray structure of the Fe(II) form of the iron superoxide dismuta... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4l2d | |||||||||
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Title | X-ray structure of the Fe(II) form of the iron superoxide dismutase from Pseudoalteromonas haloplanktis | |||||||||
Components | Superoxide dismutase [Fe] | |||||||||
Keywords | OXIDOREDUCTASE / Superoxide dismutase | |||||||||
Function / homology | Function and homology information superoxide dismutase / superoxide dismutase activity / metal ion binding Similarity search - Function | |||||||||
Biological species | Pseudoalteromonas haloplanktis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.07 Å | |||||||||
Authors | Russo Krauss, I. / Merlino, A. / Sica, F. | |||||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2014 Title: Structural and denaturation studies of two mutants of a cold adapted superoxide dismutase point to the importance of electrostatic interactions in protein stability. Authors: Merlino, A. / Russo Krauss, I. / Castellano, I. / Ruocco, M.R. / Capasso, A. / De Vendittis, E. / Rossi, B. / Sica, F. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4l2d.cif.gz | 173.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4l2d.ent.gz | 137.8 KB | Display | PDB format |
PDBx/mmJSON format | 4l2d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l2/4l2d ftp://data.pdbj.org/pub/pdb/validation_reports/l2/4l2d | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 21269.508 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudoalteromonas haloplanktis (bacteria) Gene: sodB, PSHAa1215 / Production host: Escherichia coli (E. coli) / References: UniProt: P84612, superoxide dismutase #2: Polysaccharide | alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose / trehalose / #3: Chemical | ChemComp-FE2 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.75 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Ammonium sulphate 2.0 M, NaCl 0.1 M, Hepes 0.1 M, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.07→29.2 Å / Num. all: 53308 / Num. obs: 53308 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.07→2.14 Å / % possible all: 85.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.07→29.2 Å / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.07→29.2 Å
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