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- PDB-8qnc: Crystal structure of ancestral L-galactono-1,4-lactone dehydrogen... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8qnc | ||||||
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Title | Crystal structure of ancestral L-galactono-1,4-lactone dehydrogenase: A113G variant | ||||||
![]() | L-galactono-1,4-lactone dehydrogenase: A113G variant | ||||||
![]() | FLAVOPROTEIN / biocatalysis / Vitamin C | ||||||
Function / homology | FLAVIN-ADENINE DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER![]() | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Boverio, A. / Mattevi, A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of ancestral L-galactono-1,4-lactone dehydrogenase: A113G variant Authors: Boverio, A. / Mattevi, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 119.3 KB | Display | ![]() |
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PDB format | ![]() | 88.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 782.1 KB | Display | ![]() |
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Full document | ![]() | 789.9 KB | Display | |
Data in XML | ![]() | 23 KB | Display | |
Data in CIF | ![]() | 33.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 57240.945 Da / Num. of mol.: 1 / Mutation: A113G Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: ![]() ![]() | ||||||
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#2: Chemical | ChemComp-FAD / | ||||||
#3: Chemical | #4: Chemical | ChemComp-PEG / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.4 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350, 0.2 M Lithium Nitrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Mar 31, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→66.9 Å / Num. obs: 53389 / % possible obs: 98.9 % / Redundancy: 5.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.043 / Rrim(I) all: 0.102 / Χ2: 1.02 / Net I/σ(I): 10.7 / Num. measured all: 292668 |
Reflection shell | Resolution: 1.7→1.73 Å / % possible obs: 99.4 % / Redundancy: 5.5 % / Rmerge(I) obs: 1.336 / Num. measured all: 15649 / Num. unique obs: 2825 / CC1/2: 0.593 / Rpim(I) all: 0.618 / Rrim(I) all: 1.477 / Χ2: 1.05 / Net I/σ(I) obs: 1.3 |
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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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.772 Å2
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Refinement step | Cycle: 1 / Resolution: 1.7→66.9 Å
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Refine LS restraints |
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