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Yorodumi- PDB-8qmy: Crystal structure of ancestral L-galactono-1,4-lactone dehydrogenase -
+Open data
-Basic information
Entry | Database: PDB / ID: 8qmy | ||||||
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Title | Crystal structure of ancestral L-galactono-1,4-lactone dehydrogenase | ||||||
Components | ancestral L-galactono-1,4-lactone dehydrogenase | ||||||
Keywords | FLAVOPROTEIN / Vitamin C / carbohydrate oxidase | ||||||
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: 1.9 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 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 | 8qmy.cif.gz | 302.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8qmy.ent.gz | 242.2 KB | Display | PDB format |
PDBx/mmJSON format | 8qmy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qm/8qmy ftp://data.pdbj.org/pub/pdb/validation_reports/qm/8qmy | 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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2 |
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
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-Components
#1: Protein | Mass: 57254.969 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) / References: L-galactonolactone dehydrogenase #2: Chemical | #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-PEG / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.32 Å3/Da / Density % sol: 46.91 % |
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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 X 4M / Detector: PIXEL / Date: Feb 16, 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: 1.9→48.05 Å / Num. obs: 126385 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.038 / Rrim(I) all: 0.1 / Χ2: 1.07 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 1.9→1.93 Å / % possible obs: 99.8 % / Redundancy: 6.9 % / Rmerge(I) obs: 1.734 / Num. measured all: 42710 / Num. unique obs: 6164 / CC1/2: 0.562 / Rpim(I) all: 0.702 / Rrim(I) all: 1.873 / Χ2: 1.06 / Net I/σ(I) obs: 1.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→48.05 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.445 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.143 / 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: 40.841 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→48.05 Å
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Refine LS restraints |
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