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Yorodumi- PDB-1ix9: Crystal Structure of the E. coli Manganase(III) superoxide dismut... -
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-Basic information
Entry | Database: PDB / ID: 1ix9 | ||||||
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Title | Crystal Structure of the E. coli Manganase(III) superoxide dismutase mutant Y174F at 0.90 angstroms resolution. | ||||||
Components | Superoxide Dismutase | ||||||
Keywords | OXIDOREDUCTASE / MANGANESE SUPEROXIDE DISMUTASE / Y174F MUTANT / HYDROGEN BOND / REACTIVITY | ||||||
Function / homology | Function and homology information cellular response to selenium ion / response to acidic pH / superoxide metabolic process / superoxide dismutase / superoxide dismutase activity / antioxidant activity / removal of superoxide radicals / manganese ion binding / response to heat / response to oxidative stress ...cellular response to selenium ion / response to acidic pH / superoxide metabolic process / superoxide dismutase / superoxide dismutase activity / antioxidant activity / removal of superoxide radicals / manganese ion binding / response to heat / response to oxidative stress / protein homodimerization activity / DNA binding / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.9 Å | ||||||
Authors | Anderson, B.F. / Edwards, R.A. / Whittaker, M.M. / Whittaker, J.W. / Baker, E.N. / Jameson, G.B. | ||||||
Citation | Journal: To be Published Title: Structures at 0.90 A resolution of the oxidised and reduced forms of the Y174F mutant of the manganese superoxide dismutase from Escherichia coli Authors: Anderson, B.F. / Edwards, R.A. / Whittaker, M.M. / Whittaker, J.W. / Baker, E.N. / Jameson, G.B. #1: Journal: Biochemistry / Year: 2001 Title: Removing a Hydrogen Bond in the Dimer Interface of Escherichia Coli Manganese Superoxide Dismutase Alters Structure and Reactivity Authors: Edwards, R.A. / Whittaker, M.M. / Whittaker, J.W. / Baker, E.N. / Jameson, G.B. #2: Journal: Biochemistry / Year: 2001 Title: Outer Sphere Mutations Perturb Metal Reactivity in Manganese Superoxide Dismutase Authors: Edwards, R.A. / Whittaker, M.M. / Whittaker, J.W. / Baker, E.N. / Jameson, G.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ix9.cif.gz | 222.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ix9.ent.gz | 177.5 KB | Display | PDB format |
PDBx/mmJSON format | 1ix9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ix/1ix9 ftp://data.pdbj.org/pub/pdb/validation_reports/ix/1ix9 | HTTPS FTP |
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-Related structure data
Related structure data | 1ixbC 1iohS C: citing same article (ref.) S: Starting model for refinement |
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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: 22980.877 Da / Num. of mol.: 2 / Mutation: Y174F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PDT1-5 / Production host: Escherichia coli (E. coli) / Strain (production host): QC781 / References: UniProt: P00448, superoxide dismutase #2: Chemical | #3: 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: 2.22 Å3/Da / Density % sol: 44.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 16-20% PEG6000, 0.1M BICINE, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.91 / Wavelength: 0.91 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1998 |
Radiation | Monochromator: BENT GERMANIUM SINGLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91 Å / Relative weight: 1 |
Reflection | Resolution: 0.9→30 Å / Num. all: 287367 / Num. obs: 287367 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.033 / Net I/σ(I): 41.5 |
Reflection shell | Resolution: 0.9→0.91 Å / Rmerge(I) obs: 0.355 / Mean I/σ(I) obs: 2.5 / Num. unique all: 6474 / % possible all: 67.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: MN-SOD FROM 1IOH Resolution: 0.9→30 Å / Num. parameters: 39676 / Num. restraintsaints: 44548 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS No electron density is observed for a second hydrogen atom on the coordinated solvent species in either chain. Thus, the coordinated solvent ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS No electron density is observed for a second hydrogen atom on the coordinated solvent species in either chain. Thus, the coordinated solvent species is assigned as a hydroxide ion. However, a soft vibrational mode involving a putative second hydrogen atom could render this atom undetectable in difference Fourier maps. THE CLOSE CONTACTS AND POOR GEOMETRY LISTED IN REMARK 500 ARE CAUSED BY PARTIAL OCCUPANCIES AND DISORDER.
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Solvent computation | Solvent model: P.C.MOEWS & R.H.KRETSINGER, J.MOL.BIOL.91(1975)201-228 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 41 / Occupancy sum hydrogen: 2913.71 / Occupancy sum non hydrogen: 3982.07 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.9→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 0.9→0.91 Å
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