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Open data
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Basic information
Entry | Database: PDB / ID: 1fi2 | ||||||
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Title | CRYSTAL STRUCTURE OF GERMIN (OXALATE OXIDASE) | ||||||
![]() | OXALATE OXIDASE | ||||||
![]() | OXIDOREDUCTASE / beta-jellyroll | ||||||
Function / homology | ![]() oxalate oxidase / oxalate oxidase activity / superoxide dismutase complex / apoplast / superoxide dismutase activity / removal of superoxide radicals / cell wall organization / manganese ion binding / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Woo, E.J. / Dunwell, J.M. / Goodenough, P.W. / Marvier, A.C. / Pickersgill, R.W. | ||||||
![]() | ![]() Title: Germin is a manganese containing homohexamer with oxalate oxidase and superoxide dismutase activities. Authors: Woo, E.J. / Dunwell, J.M. / Goodenough, P.W. / Marvier, A.C. / Pickersgill, R.W. #1: ![]() Title: Barley Oxalate Oxidase is a Hexameric Protein Related to Seed Storage Proteins: Evidence from X-ray Crystallography Authors: Woo, E.J. / Dunwell, J.M. / Goodenough, P.W. / Pickersgill, R.W. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 52.2 KB | Display | ![]() |
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PDB format | ![]() | 40.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | |
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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
#1: Protein | Mass: 21237.170 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: Chemical | ChemComp-MN / |
#3: Water | ChemComp-HOH / |
Compound details | The germin dimer is structurally related to the 7S seed storage protein monomer (eg phaseolin ...The germin dimer is structurally related to the 7S seed storage protein monomer (eg phaseolin monomer). Each germin monomer binds a single manganese ion. |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 33 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 301 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 2.2 M ammonium sulfate, 5% 2-propanol, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 301K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / pH: 5.3 / Details: Woo, E.J., (1998) FEBS Lett., 437, 87. | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.6→12 Å / Num. all: 24846 / Num. obs: 23707 / % possible obs: 95.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 14 % / Biso Wilson estimate: 17 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 24.4 | ||||||||||||||||||
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 5 % / Rmerge(I) obs: 0.083 / Num. unique all: 2084 / % possible all: 85.3 | ||||||||||||||||||
Reflection shell | *PLUS % possible obs: 85.3 % |
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Processing
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 1.6→12.4 Å
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Refine LS restraints |
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