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- PDB-1wb7: Iron Superoxide Dismutase (Fe-SOD) From The Hyperthermophile Sulf... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1wb7 | ||||||
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Title | Iron Superoxide Dismutase (Fe-SOD) From The Hyperthermophile Sulfolobus Solfataricus. Crystal Structure of the Y41F mutant. | ||||||
![]() | SUPEROXIDE DISMUTASE [FE] | ||||||
![]() | OXIDOREDUCTASE / SUPEROXIDE DISMUTASE / SOD / IRON / SUPEROXIDE RADICAL DISPROPORTIONATION / SULFOLOBUS SOLFTARICUS / THERMOSTABLE | ||||||
Function / homology | ![]() superoxide dismutase / superoxide dismutase activity / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gogliettino, M.A. / Tanfani, F. / Scire, A. / Ursby, T. / Adinolfi, B.S. / Cacciamani, T. / De Vendittis, E. | ||||||
![]() | ![]() Title: The Role of Tyr41 and His155 in the Functional Properties of Superoxide Dismutase from the Archaeon Sulfolobus Solfataricus Authors: Gogliettino, M.A. / Tanfani, F. / Scire, A. / Ursby, T. / Adinolfi, B.S. / Cacciamani, T. / De Vendittis, E. #1: ![]() Title: Iron Superoxide Dismutase from the Archaeon Sulfolobus Solfataricus: Analysis of Structure and Thermostability Authors: Ursby, T. / Adinolfi, B.S. / Al-Karadaghi, S. / De Vendittis, E. / Bocchini, V. #2: Journal: Eur.J.Biochem. / Year: 2001 Title: Phenylmethanesulfonyl Fluoride Inactivates an Archaeal Superoxide Dismutase by Chemical Modification of a Specific Tyrosine Residue Authors: De Vendittis, E. / Ursby, T. / Rullo, R. / Gogliettino, M.A. / Masullo, M. / Bocchini, V. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 99.5 KB | Display | ![]() |
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PDB format | ![]() | 75.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1sss S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.90759, -0.000509, 0.419858), Vector: |
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Components
#1: Protein | Mass: 24126.312 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | Compound details | ENGINEERED | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: CRYSTALS WERE GROWN BY VAPOR DIFFUSION IN HANGING DROPS AT 21C IN A 1 TO 1 MIX OF THE RESERVOIR SOLUTION (8% PEG 8000, 0.1 M TRIS/HCL PH 8.5) AND A PROTEIN SOLUTION (1.45 MG/ML Y41F-SSSOD, ...Details: CRYSTALS WERE GROWN BY VAPOR DIFFUSION IN HANGING DROPS AT 21C IN A 1 TO 1 MIX OF THE RESERVOIR SOLUTION (8% PEG 8000, 0.1 M TRIS/HCL PH 8.5) AND A PROTEIN SOLUTION (1.45 MG/ML Y41F-SSSOD, 20 MM TRIS/HCL PH 7.8, 1% GLYCEROL). | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 21 ℃ / pH: 7.8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 24, 1998 / Details: PT-COATED MIRROR AND SI MONOCHROMATOR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.986 Å / Relative weight: 1 |
Reflection | Resolution: 2.24→60.9 Å / Num. obs: 19994 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 12.4 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 2.24→2.39 Å / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 5.2 / % possible all: 99.8 |
Reflection | *PLUS Lowest resolution: 60.9 Å / Rmerge(I) obs: 0.093 |
Reflection shell | *PLUS Rmerge(I) obs: 0.255 / Mean I/σ(I) obs: 5.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1SSS ![]() 1sss Resolution: 2.24→29.07 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1649340.81 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Stereochemistry target values: MAXIMUM LIKELIHOOD USING AMPLITUDES Details: NOTE THAT RESIDUES 1-3 AND 209- -210 OF THE COMPLETE SEQUENCE ARE MISSING IN THIS ENTRY DUE TO DISORDER IN THE CRYSTAL. THE NCS USED IN THE REFINEMENT INCLUDED MOLECULE A EXCEPT 7 RESIDUES, ...Details: NOTE THAT RESIDUES 1-3 AND 209- -210 OF THE COMPLETE SEQUENCE ARE MISSING IN THIS ENTRY DUE TO DISORDER IN THE CRYSTAL. THE NCS USED IN THE REFINEMENT INCLUDED MOLECULE A EXCEPT 7 RESIDUES, THE IRON ION AND 48 WATER MOLECULES AND THE CORRESPONDING NCS RELEATED ATOMS. THE RMS DEVIATION FOR THE ATOMS USED FOR NCS IN THE REFINEMENT IS 0.005 A.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.5933 Å2 / ksol: 0.380503 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.24→29.07 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.24→2.38 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Rfactor Rfree: 0.222 / Rfactor Rwork: 0.18 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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