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Open data
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Basic information
Entry | Database: PDB / ID: 1ryi | |||||||||
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Title | STRUCTURE OF GLYCINE OXIDASE WITH BOUND INHIBITOR GLYCOLATE | |||||||||
![]() | GLYCINE OXIDASE | |||||||||
![]() | OXIDOREDUCTASE / FLAVOPROTEIN / OXIDASE / PROTEIN-INHIBITOR COMPLEX | |||||||||
Function / homology | ![]() glycine oxidase / glycine oxidase activity / thiamine diphosphate biosynthetic process / thiamine biosynthetic process / amino acid metabolic process / response to herbicide / FAD binding / oxidoreductase activity / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Moertl, M. / Diederichs, K. / Welte, W. / Pollegioni, L. / Molla, G. / Motteran, L. / Andriolo, G. / Pilone, M.S. | |||||||||
![]() | ![]() Title: Structure-function correlation in glycine oxidase from Bacillus subtilis Authors: Moertl, M. / Diederichs, K. / Welte, W. / Molla, G. / Motteran, L. / Andriolo, G. / Pilone, M.S. / Pollegioni, L. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 323.6 KB | Display | ![]() |
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PDB format | ![]() | 259.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 64 KB | Display | |
Data in CIF | ![]() | 91.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-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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2 | ![]()
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Unit cell |
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Details | THE BIOLOGICAL ASSEMBLY IS A TETRAMER. THERE ARE TWO DIFFERENT TETRAMERS IN THE CRYSTAL. THE SECOND PART OF THE FIRST TETRAMER, WICH IS COMPOSED OF CHAIN A AND B AND IT'S SYMMETRY EQUIVALENTS, IS GENERATED BY THE TWO FOLD AXIS x, -y+2, -z+2. THE SECOND PART OF THE SECOND TETRAMER, WICH IS COMPOSED OF CHAIN C AND D AND IT'S SYMMETRY EQUIVALENTS, IS GENERATED BY THE TWO FOLD AXIS -x, y, -z+3/2. |
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Components
#1: Protein | Mass: 42636.719 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-FAD / #3: Chemical | ChemComp-GOA / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.5 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.2 Details: 10% w/v PEG 1000, 100 mM Imidazole, 200 mM Ca-Acetate, 30 mM Sodium-Glycolate, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 28, 2003 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→19.92 Å / Num. all: 159578 / Num. obs: 159578 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.8→1.9 Å / % possible all: 96.5 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 25.85 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→19.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.846 Å / Total num. of bins used: 20 /
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