+Open data
-Basic information
Entry | Database: PDB / ID: 8ate | ||||||
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Title | Galacturonic acid oxidase from Citrus sinensis | ||||||
Components | FAD-binding PCMH-type domain-containing protein | ||||||
Keywords | FLAVOPROTEIN / Carbohydrate oxidation | ||||||
Function / homology | FLAVIN-ADENINE DINUCLEOTIDE / IODIDE ION / DI(HYDROXYETHYL)ETHER Function and homology information | ||||||
Biological species | Citrus sinensis (sweet orange) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å | ||||||
Authors | Boverio, A. / Savino, S. / Fraaije, M.W. / Loncar, N. | ||||||
Funding support | 1items
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Citation | Journal: Chemcatchem / Year: 2023 Title: Biochemical and Structural Characterization of a Uronic Acid Oxidase from Citrus sinensis Authors: Boverio, A. / van Beek, H.L. / Savino, S. / Ranoux, A. / Huijgen, W.J.J. / Raaijmakers, H.W.C. / Fraaije, M.W. / Loncar, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ate.cif.gz | 118.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ate.ent.gz | 88.4 KB | Display | PDB format |
PDBx/mmJSON format | 8ate.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/at/8ate ftp://data.pdbj.org/pub/pdb/validation_reports/at/8ate | 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
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 57324.457 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Citrus sinensis (sweet orange) / Gene: CISIN_1g015646mg / Cell line (production host): X-33 / Production host: Komagataella pastoris (fungus) |
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#3: Sugar | ChemComp-NAG / |
-Non-polymers , 7 types, 92 molecules
#2: Chemical | ChemComp-FAD / | ||||||||
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#4: Chemical | ChemComp-CL / | ||||||||
#5: Chemical | #6: Chemical | #7: Chemical | ChemComp-GOL / | #8: Chemical | ChemComp-PEG / | #9: Water | ChemComp-HOH / | |
-Details
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: 2.83 Å3/Da / Density % sol: 56.53 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.2 M NaI, 20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.96546 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Apr 13, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96546 Å / Relative weight: 1 |
Reflection | Resolution: 1.92→108.75 Å / Num. obs: 45258 / % possible obs: 90 % / Redundancy: 15.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.022 / Rrim(I) all: 0.089 / Χ2: 1.03 / Net I/σ(I): 16.9 / Num. measured all: 714593 |
Reflection shell | Resolution: 1.92→1.96 Å / % possible obs: 99.4 % / Redundancy: 16.2 % / Rmerge(I) obs: 2.84 / Num. measured all: 53533 / Num. unique obs: 3312 / CC1/2: 0.63 / Rpim(I) all: 0.724 / Rrim(I) all: 2.932 / Χ2: 1.11 / Net I/σ(I) obs: 1.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: alpha fold Resolution: 1.92→88.03 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.447 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.154 / 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: 50.267 Å2
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Refinement step | Cycle: 1 / Resolution: 1.92→88.03 Å
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Refine LS restraints |
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