+Open data
-Basic information
Entry | Database: PDB / ID: 5k8e | |||||||||
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Title | Xylooligosaccharide oxidase from Myceliophthora thermophila C1 | |||||||||
Components | FAD linked oxidase-like protein | |||||||||
Keywords | OXIDOREDUCTASE / FAD / CAZy / oligosaccharide / xylose / xylan | |||||||||
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 | Myceliophthora thermophila (fungus) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.93 Å | |||||||||
Authors | Rozeboom, H.J. / Ferrari, A.R. / Fraaije, M.W. | |||||||||
Funding support | Netherlands, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2016 Title: Discovery of a Xylooligosaccharide Oxidase from Myceliophthora thermophila C1. Authors: Ferrari, A.R. / Rozeboom, H.J. / Dobruchowska, J.M. / van Leeuwen, S.S. / Vugts, A.S. / Koetsier, M.J. / Visser, J. / 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 | 5k8e.cif.gz | 207.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5k8e.ent.gz | 164 KB | Display | PDB format |
PDBx/mmJSON format | 5k8e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k8/5k8e ftp://data.pdbj.org/pub/pdb/validation_reports/k8/5k8e | HTTPS FTP |
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-Related structure data
Related structure data | 5l6fC 5l6gC 1zr6S 3rj8S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 54376.484 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: First 16 residues are a signal sequence Source: (gene. exp.) Myceliophthora thermophila (strain ATCC 42464 / BCRC 31852 / DSM 1799) (fungus) Gene: MYCTH_102971 Production host: Myceliophthora thermophila ATCC 42464 (fungus) References: UniProt: G2QG48, Oxidoreductases; Acting on the CH-OH group of donors; With oxygen as acceptor |
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-Sugars , 2 types, 5 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Sugar | |
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-Non-polymers , 4 types, 376 molecules
#3: Chemical | ChemComp-FAD / | ||
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#5: Chemical | ChemComp-MES / | ||
#6: Chemical | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 15-18% PEG3350, 0.1 M MES buffer, 0.2 M ammonium chloride |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.54 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 9, 2015 |
Radiation | Monochromator: HeliosMX mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→53.6 Å / Num. obs: 37594 / % possible obs: 99.4 % / Redundancy: 7.2 % / Biso Wilson estimate: 7.1 Å2 / Rmerge(I) obs: 0.163 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 1.93→1.97 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.673 / Mean I/σ(I) obs: 2.4 / % possible all: 91.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ZR6 and 3RJ8 Resolution: 1.93→53.6 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.943 / SU B: 6.801 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.132 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.949 Å2
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Refinement step | Cycle: 1 / Resolution: 1.93→53.6 Å
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Refine LS restraints |
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