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Yorodumi- PDB-1avm: THE CAMBIALISTIC SUPEROXIDE DISMUTASE (FE-SOD) OF P. SHERMANII CO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1avm | ||||||
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Title | THE CAMBIALISTIC SUPEROXIDE DISMUTASE (FE-SOD) OF P. SHERMANII COORDINATED BY AZIDE | ||||||
Components | SUPEROXIDE DISMUTASE | ||||||
Keywords | OXIDOREDUCTASE / SOD / SUPEROXIDE DISMUTASE / PROPIONIBACTERIUM SHERMANII / AZIDE | ||||||
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 / ISOMORPHOUS WITH FE-SOD OF P.SHERMANII / Resolution: 1.55 Å | ||||||
Authors | Schmidt, M. / Parak, F. | ||||||
Citation | Journal: Inorg.Chim.Acta. / Year: 1998 Title: The Structure of the Azide Coordinated Superoxide Dismutase of P. Shermanii Investigated by X-Ray Structure Analysis, Exafs, Mossbauer-and Epr Spectroscopy Authors: Schmidt, M. / Scherk, C. / Iakovleva, O. / Nolting, H.F. / Meier, B. / Parak, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1avm.cif.gz | 96.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1avm.ent.gz | 76.8 KB | Display | PDB format |
PDBx/mmJSON format | 1avm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/av/1avm ftp://data.pdbj.org/pub/pdb/validation_reports/av/1avm | HTTPS FTP |
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-Related structure data
Related structure data | 1ar5S 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 on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.2025, -0.0016, -0.9793), Vector: |
-Components
#1: Protein | Mass: 22659.326 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Propionibacterium freudenreichii subsp. shermanii (bacteria) Species: Propionibacterium freudenreichii / Strain: PZ3 / Description: GERMAN COLLECTION OF MICROORGANISMS (DSM) / 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: 2.06 Å3/Da / Density % sol: 31.7 % | |||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion - hanging drop - microseeding / pH: 6.15 Details: FROM 2.15 M (NH4)2SO4, 55 MG/ML PROTEIN, 4 DEG C, PH 6.15, HANGING DROP, MICROSEED FROM NATIVE FE-SOD OF P.SHERM., SOAKED FOR 24 H IN 150 MM SODIUM AZIDE, vapor diffusion - hanging drop - ...Details: FROM 2.15 M (NH4)2SO4, 55 MG/ML PROTEIN, 4 DEG C, PH 6.15, HANGING DROP, MICROSEED FROM NATIVE FE-SOD OF P.SHERM., SOAKED FOR 24 H IN 150 MM SODIUM AZIDE, vapor diffusion - hanging drop - microseeding, temperature 277K | |||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 6.1 / Method: vapor diffusion, hanging drop / Details: Schmidt, M., (1996) J.Biol.Inorg.Chem., 1, 532. | |||||||||||||||
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: Mar 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→39.8 Å / Num. obs: 45471 / % possible obs: 84.6 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 14 Å2 / Rmerge(I) obs: 0.044 / Rsym value: 0.044 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 1.55→1.6 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.158 / Mean I/σ(I) obs: 4.8 / Rsym value: 0.158 / % possible all: 61.9 |
Reflection | *PLUS Num. obs: 47159 / Num. measured all: 183083 / Rmerge(I) obs: 0.042 |
-Processing
Software |
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Refinement | Method to determine structure: ISOMORPHOUS WITH FE-SOD OF P.SHERMANII Starting model: PDB ENTRY 1AR5 Resolution: 1.55→8 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 4.5 Details: REFINEMENT OF THE CENTRAL IRON, THE COORDINATING SOLVENT AND THE AZIDE MOLECULE UNRESTRAINED
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Displacement parameters | Biso mean: 15.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.16 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→8 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NO RESTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 7.7 Å / Rfactor obs: 0.166 / Rfactor Rfree: 0.195 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.22 |