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Yorodumi- PDB-1ogp: The crystal structure of plant sulfite oxidase provides insight i... -
+Open data
-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 | ||||||
Components | SULFITE OXIDASE | ||||||
Keywords | OXIDOREDUCTASE / MOLYBDENUM COFACTOR / MOLYBDOPTERIN / PLANT SULFITE OXIDASE / PEROXISOMES / INTRAMOLECULAR ELECTRON TRANSFER / OXIDOREDUCTAS | ||||||
Function / homology | Function and homology information 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 | ARABIDOPSIS THALIANA (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Schrader, N. / Fischer, K. / Theis, K. / Mendel, R.R. / Schwarz, G. / Kisker, C. | ||||||
Citation | Journal: Structure / Year: 2003 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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ogp.cif.gz | 474.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ogp.ent.gz | 387.7 KB | Display | PDB format |
PDBx/mmJSON format | 1ogp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/og/1ogp ftp://data.pdbj.org/pub/pdb/validation_reports/og/1ogp | HTTPS FTP |
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-Related structure data
Related structure data | 1soxS S: Starting model for refinement |
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Similar structure data |
-Links
-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.) ARABIDOPSIS THALIANA (thale cress) / Plasmid: PQE80 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TP1000 / References: UniProt: Q9S850, sulfite oxidase #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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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