+Open data
-Basic information
Entry | Database: PDB / ID: 1bs3 | ||||||
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Title | P.SHERMANII SOD(FE+3) FLUORIDE | ||||||
Components | SUPEROXIDE DISMUTASE | ||||||
Keywords | OXIDOREDUCTASE / SUPEROXIDE DISMUTASE / FLUORIDE | ||||||
Function / homology | Function and homology information superoxide dismutase / superoxide dismutase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Propionibacterium freudenreichii subsp. shermanii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.55 Å | ||||||
Authors | Schmidt, M. | ||||||
Citation | Journal: Eur.J.Biochem. / Year: 1999 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bs3.cif.gz | 97.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bs3.ent.gz | 77.9 KB | Display | PDB format |
PDBx/mmJSON format | 1bs3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bs/1bs3 ftp://data.pdbj.org/pub/pdb/validation_reports/bs/1bs3 | HTTPS FTP |
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-Related structure data
Related structure data | 1bsmC 1bt8C 1ar5S S: Starting model for refinement C: citing same article (ref.) |
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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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.2028, -0.0019, -0.9792), Vector: |
-Components
#1: Protein | Mass: 22659.326 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: COMPETITIVELY INHIBITED BY FLOURIDE. FLUORIDE OCCUPIES SUBSTRATE BINDING SITE. Source: (natural) Propionibacterium freudenreichii subsp. shermanii (bacteria) Cellular location: CYTOPLASM / Species: Propionibacterium freudenreichii / Strain: PZ3 / References: UniProt: P80293, superoxide dismutase #2: Chemical | #3: Chemical | #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 Å3/Da / Density % sol: 32 % | |||||||||||||||||||||||||
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Crystal grow | pH: 6.1 / Details: pH 6.1 | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / 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: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Sep 1, 1997 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→39.7 Å / Num. obs: 45799 / % possible obs: 83.1 % / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Biso Wilson estimate: 13.7 Å2 / Rsym value: 0.034 / Net I/σ(I): 18 |
Reflection shell | Resolution: 1.55→1.62 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 7.6 / Rsym value: 0.148 / % possible all: 67 |
Reflection | *PLUS Num. obs: 45923 / % possible obs: 78 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.036 |
-Processing
Software |
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Refinement | Starting model: PDB ENTRY 1AR5 Resolution: 1.55→9 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3.5 / Details: IRON AND FLUORIDE REFINED UNRESTRAINED
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Displacement parameters | Biso mean: 14.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.15 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.62 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.17 / Rfactor Rfree: 0.208 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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