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Yorodumi- PDB-8qnc: Crystal structure of ancestral L-galactono-1,4-lactone dehydrogen... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8qnc | ||||||
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Title | Crystal structure of ancestral L-galactono-1,4-lactone dehydrogenase: A113G variant | ||||||
Components | L-galactono-1,4-lactone dehydrogenase: A113G variant | ||||||
Keywords | FLAVOPROTEIN / biocatalysis / Vitamin C | ||||||
Function / homology | FLAVIN-ADENINE DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Boverio, A. / Mattevi, A. | ||||||
Funding support | Italy, 1items
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Citation | Journal: To Be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8qnc.cif.gz | 119.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8qnc.ent.gz | 88.7 KB | Display | PDB format |
PDBx/mmJSON format | 8qnc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qn/8qnc ftp://data.pdbj.org/pub/pdb/validation_reports/qn/8qnc | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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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: Escherichia coli (E. coli) / References: L-galactonolactone dehydrogenase | ||||||
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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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9677 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→66.9 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.473 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.106 / 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: 1.2 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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