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- PDB-1ogp: The crystal structure of plant sulfite oxidase provides insight i... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ogp | ||||||
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Title | The crystal structure of plant sulfite oxidase provides insight into sulfite oxidation in plants and animals | ||||||
![]() | SULFITE OXIDASE | ||||||
![]() | OXIDOREDUCTASE / MOLYBDENUM COFACTOR / MOLYBDOPTERIN / PLANT SULFITE OXIDASE / PEROXISOMES / INTRAMOLECULAR ELECTRON TRANSFER / OXIDOREDUCTAS | ||||||
Function / homology | ![]() response to sulfur dioxide / sulfite oxidase / sulfite oxidase activity / chlorophyll metabolic process / sulfur compound metabolic process / molybdenum ion binding / molybdopterin cofactor binding / peroxisome / heme binding / mitochondrion / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Schrader, N. / Fischer, K. / Theis, K. / Mendel, R.R. / Schwarz, G. / Kisker, C. | ||||||
![]() | ![]() Title: The Crystal Structure of Plant Sulfite Oxidase Provides Insights Into Sulfite Oxidation in Plants and Animals Authors: Schrader, N. / Fischer, K. / Theis, K. / Mendel, R.R. / Schwarz, G. / Kisker, C. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 474.7 KB | Display | ![]() |
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PDB format | ![]() | 387.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.6 MB | Display | ![]() |
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Full document | ![]() | 2.7 MB | Display | |
Data in XML | ![]() | 102.8 KB | Display | |
Data in CIF | ![]() | 132.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1soxS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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3 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 43381.098 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Details: ONE MOLYBDENUMN COFACTOR IN EACH MOLECULE / Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-CS / #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-MTQ / ( #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.7 Å3/Da / Density % sol: 78 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 9.2 Details: 5-12% JEFFAMINE 600, 50 MM TRIS/HCL, 10 MM CSCL, PH 9.2 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / pH: 9.2 / Method: vapor diffusion | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Oct 15, 2002 / Details: BENT CONICAL SI-MIRROR |
Radiation | Monochromator: BENT CYLINDRICAL GE(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→30 Å / Num. obs: 199819 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 5.9 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 21.6 |
Reflection shell | Resolution: 2.55→2.64 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.887 / Mean I/σ(I) obs: 2.03 / % possible all: 99.5 |
Reflection | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 30 Å / Num. measured all: 1177360 / Rmerge(I) obs: 0.11 |
Reflection shell | *PLUS % possible obs: 99.5 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1SOX Resolution: 2.6→182.57 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.893 / SU B: 8.128 / SU ML: 0.174 / Cross valid method: THROUGHOUT / ESU R: 0.268 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.49 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→182.57 Å
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Refine LS restraints |
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