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Yorodumi- PDB-1ar4: X-RAY STRUCTURE ANALYSIS OF THE CAMBIALISTIC SUPEROXIDE DISMUTASE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ar4 | ||||||
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Title | X-RAY STRUCTURE ANALYSIS OF THE CAMBIALISTIC SUPEROXIDE DISMUTASE FROM PROPIONIBACTERIUM SHERMANII ACTIVE WITH FE OR MN | ||||||
Components | SUPEROXIDE DISMUTASE | ||||||
Keywords | OXIDOREDUCTASE / SUPEROXIDE DISMUTASE / DEGRADES O2- / DISMUTASE | ||||||
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: 1.9 Å | ||||||
Authors | Schmidt, M. / Meier, B. / Parak, F. | ||||||
Citation | Journal: J.Biol.Inorg.Chem. / Year: 1996 Title: X-Ray Structure of the Cambialistic Superoxide Dismutase from Propionibacterium Shermanii Active with Fe or Mn Authors: Schmidt, M. / 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 | 1ar4.cif.gz | 100.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ar4.ent.gz | 77.5 KB | Display | PDB format |
PDBx/mmJSON format | 1ar4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ar4_validation.pdf.gz | 369.2 KB | Display | wwPDB validaton report |
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Full document | 1ar4_full_validation.pdf.gz | 376.4 KB | Display | |
Data in XML | 1ar4_validation.xml.gz | 9.9 KB | Display | |
Data in CIF | 1ar4_validation.cif.gz | 16.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ar/1ar4 ftp://data.pdbj.org/pub/pdb/validation_reports/ar/1ar4 | HTTPS FTP |
-Related structure data
Similar structure data |
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-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: (0.2036, -0.0003, -0.9791), Vector: |
-Components
#1: Protein | Mass: 22659.326 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: GERMAN COLLECTION OF MICROORGANISMS (DSM) Source: (natural) Propionibacterium freudenreichii subsp. shermanii (bacteria) Species: Propionibacterium freudenreichii / Strain: subsp. shermanii / References: UniProt: P80293, superoxide dismutase #2: Chemical | #3: Water | ChemComp-HOH / | Nonpolymer details | THE CHARGE OF MANGANESE IS NOT YET KNOWN UNAMBIGUOU | |
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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: 2.05 Å3/Da / Density % sol: 32 % | |||||||||||||||
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Crystal grow | Temperature: 277 K / Method: microseeding / pH: 6.1 Details: PROTEIN WAS CRYSTALLIZED AT 50MG/ML FROM 2.15 M (NH4)2SO4, 50 MM KPI, PH 6.15, 4 DEG C, NUCLEATION INDUCED BY MICROSEEDING FROM CRYSTALS GROWN FROM 14MG/ML PROTEIN, 2.4 M (NH4)2SO4, 50 MM ...Details: PROTEIN WAS CRYSTALLIZED AT 50MG/ML FROM 2.15 M (NH4)2SO4, 50 MM KPI, PH 6.15, 4 DEG C, NUCLEATION INDUCED BY MICROSEEDING FROM CRYSTALS GROWN FROM 14MG/ML PROTEIN, 2.4 M (NH4)2SO4, 50 MM KPI, PH 7.4, 4 DEG C., microseeding, temperature 277K PH range: 6.15 (7.4 for microseeds) | |||||||||||||||
Crystal | *PLUS | |||||||||||||||
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 HI-STAR / Detector: AREA DETECTOR / Date: Dec 1, 1997 / Details: NO |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→12.8 Å / Num. obs: 26323 / % possible obs: 89.2 % / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Biso Wilson estimate: 16.68 Å2 / Rmerge(I) obs: 0.042 / Rsym value: 0.042 / Net I/σ(I): 17 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.042 / Mean I/σ(I) obs: 5.3 / Rsym value: 0.042 / % possible all: 72.3 |
Reflection | *PLUS Num. measured all: 81457 |
Reflection shell | *PLUS % possible obs: 72.3 % |
-Processing
Software |
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Refinement | Method to determine structure: ISOMORPHOUS WITH FE-SOD OF P.SHERMANII Starting model: FE-SOD OF P.SHERMANII Resolution: 1.9→9 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 4.5 Details: MN CENTER REFINED WITHOUT VDW AND DISTANCE RESTRAINTS
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Displacement parameters | Biso mean: 15.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.18 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→9 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: UNRESTRAINED | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→1.99 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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