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- PDB-1en5: CRYSTAL STRUCTURE ANALYSIS OF THE E. COLI MANGANESE SUPEROXIDE DI... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1en5 | ||||||
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Title | CRYSTAL STRUCTURE ANALYSIS OF THE E. COLI MANGANESE SUPEROXIDE DISMUTASE Y34F MUTANT | ||||||
![]() | MANGANESE SUPEROXIDE DISMUTASE | ||||||
![]() | OXIDOREDUCTASE / proton shuttle / Y34F / mutant / manganese superoxide dismutase | ||||||
Function / homology | ![]() 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Edwards, R.A. / Whittaker, M.M. / Baker, E.N. / Whittaker, J.W. / Jameson, G.B. | ||||||
![]() | ![]() 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. #1: ![]() 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: ![]() Title: Crystal Structure of Escherichia coli Manganese Superoxide Dismutase at 2.1 A Resolution Authors: Edwards, R.A. / Baker, H.M. / Whittaker, M.M. / Whittaker, J.W. / Jameson, G.B. / Baker, E.N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 172.1 KB | Display | ![]() |
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PDB format | ![]() | 139.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 437.7 KB | Display | ![]() |
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Full document | ![]() | 442.3 KB | Display | |
Data in XML | ![]() | 31.7 KB | Display | |
Data in CIF | ![]() | 44.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 22980.879 Da / Num. of mol.: 4 / Mutation: Y34F Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-MN / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.94 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.3 Details: 20% w/v PEG 6000, 0.1 M bicine, 25 mM sodium azide, pH 8.3, VAPOR DIFFUSION, SITTING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Mar 25, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→38.85 Å / Num. all: 43949 / Num. obs: 43949 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 16.7 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 2.3→2.33 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.298 / Num. unique all: 1198 / % possible all: 79.2 |
Reflection | *PLUS Num. measured all: 348981 |
Reflection shell | *PLUS % possible obs: 79.2 % / Mean I/σ(I) obs: 3.2 |
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Processing
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Refinement | Resolution: 2.3→40 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.3→40 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 40 Å / σ(F): 0 / % reflection Rfree: 5.1 % / Rfactor obs: 0.167 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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