+Open data
-Basic information
Entry | Database: PDB / ID: 6y0r | ||||||
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Title | Chitooligosaccharide oxidase | ||||||
Components | Chitooligosaccharide oxidase | ||||||
Keywords | OXIDOREDUCTASE / Flavin-dependent / oxidase / oligosaccharides / covalent FAD | ||||||
Function / homology | Function and homology information Oxidoreductases; Acting on the CH-OH group of donors; With oxygen as acceptor / FAD binding / oxidoreductase activity / extracellular region Similarity search - Function | ||||||
Biological species | Gibberella zeae (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.611 Å | ||||||
Authors | Savino, S. / Fraaije, M.W. | ||||||
Citation | Journal: Febs Lett. / Year: 2020 Title: Analysis of the structure and substrate scope of chitooligosaccharide oxidase reveals high affinity for C2-modified glucosamines. Authors: Savino, S. / Jensen, S. / Terwisscha van Scheltinga, A. / Fraaije, M.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6y0r.cif.gz | 184.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6y0r.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6y0r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6y0r_validation.pdf.gz | 778.5 KB | Display | wwPDB validaton report |
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Full document | 6y0r_full_validation.pdf.gz | 784.1 KB | Display | |
Data in XML | 6y0r_validation.xml.gz | 22.7 KB | Display | |
Data in CIF | 6y0r_validation.cif.gz | 33.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y0/6y0r ftp://data.pdbj.org/pub/pdb/validation_reports/y0/6y0r | HTTPS FTP |
-Related structure data
Related structure data | 1zr6S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 52668.340 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: FAD Source: (gene. exp.) Gibberella zeae (strain PH-1 / ATCC MYA-4620 / FGSC 9075 / NRRL 31084) (fungus) Gene: chitO, FGRAMPH1_01T20975 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: I1S2K2, Oxidoreductases; Acting on the CH-OH group of donors; With oxygen as acceptor |
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#2: Chemical | ChemComp-FAD / |
#3: 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: 2.52 Å3/Da / Density % sol: 51.25 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 0.3 M Calcium Chloride, 0.1 M Bis-Tris pH 5.7, 34% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.0098 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 20, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0098 Å / Relative weight: 1 |
Reflection | Resolution: 1.611→48.626 Å / Num. obs: 67366 / % possible obs: 96.84 % / Redundancy: 2 % / CC1/2: 1 / Net I/σ(I): 20.59 |
Reflection shell | Resolution: 1.611→1.668 Å / Num. unique obs: 5457 / CC1/2: 0.698 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1zr6 Resolution: 1.611→48.626 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.96 / Cross valid method: FREE R-VALUE / ESU R: 0.082 / ESU R Free: 0.081 Details: Hydrogens have been added in their 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.589 Å2
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Refinement step | Cycle: LAST / Resolution: 1.611→48.626 Å
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Refine LS restraints |
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LS refinement shell |
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