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Open data
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Basic information
Entry | Database: PDB / ID: 1bt8 | ||||||
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Title | P.SHERMANII SOD(FE+3) PH 10.0 | ||||||
![]() | SUPEROXIDE DISMUTASE | ||||||
![]() | OXIDOREDUCTASE / SUPEROXIDE DISMUTASE | ||||||
Function / homology | ![]() superoxide dismutase / superoxide dismutase activity / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Schmidt, M. | ||||||
![]() | ![]() Title: Manipulating the coordination mumber of the ferric iron within the cambialistic superoxide dismutase of Propionibacterium shermanii by changing the pH-value A crystallographic analysis Authors: Schmidt, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 96 KB | Display | ![]() |
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PDB format | ![]() | 74.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1bs3C ![]() 1bsmC ![]() 1ar5S S: Starting model for refinement C: citing same article ( |
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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: (0.4338, 0.0029, -0.901), Vector: |
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Components
#1: Protein | Mass: 22659.326 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() Cellular location: CYTOPLASM / Species: Propionibacterium freudenreichii / Strain: PZ3 / References: UniProt: P80293, superoxide dismutase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 32 % | |||||||||||||||||||||||||
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Crystal grow | pH: 10 / Details: pH 10.0 | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 6.1 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ![]() |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: May 1, 1998 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→40.2 Å / Num. obs: 22958 / % possible obs: 70.8 % / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Biso Wilson estimate: 15.4 Å2 / Rsym value: 0.059 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 1.85→1.91 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 5.1 / Rsym value: 0.147 / % possible all: 57.2 |
Reflection | *PLUS Num. obs: 22966 / % possible obs: 71 % / Rmerge(I) obs: 0.059 |
Reflection shell | *PLUS % possible obs: 57.2 % / Rmerge(I) obs: 0.147 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1AR5 Resolution: 1.85→8.5 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3.5 Details: IRON AND COORDINATED SOLVENT MOLECULES REFINED UNRESTRAINED THE IRON IONS AND THE COORDINATING SOLVENT MOLECULES WERE REFINED WITHOUT RESTRAINTS
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Displacement parameters | Biso mean: 17.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.23 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→8.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.93 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.174 / Rfactor Rfree: 0.227 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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