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Yorodumi- PDB-8tx5: Crystal structure of an engineered variant of galactose oxidase, ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8tx5 | ||||||
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Title | Crystal structure of an engineered variant of galactose oxidase, GOaseRd4BB, from Fusarium graminearum | ||||||
Components | Galactose oxidase | ||||||
Keywords | OXIDOREDUCTASE / galactose oxidase / Islatravir / Aerobic Oxidation / Biocatalytic oxidation / (R)-ethynyl-glyceraldehyde 3-phosphate | ||||||
Function / homology | Function and homology information galactose oxidase / galactose oxidase activity / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Fusarium graminearum (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å | ||||||
Authors | Selvaraj, B. / Orth, P. | ||||||
Funding support | United States, 1items
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Citation | Journal: Chemrxiv / Year: 2023 Title: Development of a Biocatalytic Aerobic Oxidation for the Manufacturing Route to Islatravir Authors: Shaw, M.H. / Fryszkowska, A. / Alvizo, O. / Attadgie, I. / Borra-Garske, M. / Devine, P.N. / Duan, D. / Grosser, S.T. / Forstater, J.H. / Hughes, G.J. / Maloney, K.M. / Margelefsky, E. / ...Authors: Shaw, M.H. / Fryszkowska, A. / Alvizo, O. / Attadgie, I. / Borra-Garske, M. / Devine, P.N. / Duan, D. / Grosser, S.T. / Forstater, J.H. / Hughes, G.J. / Maloney, K.M. / Margelefsky, E. / Mattern, K.A. / Miller, M.T. / Nawrat, C.C. / Nazor, J. / Orth, P. / Ouimet, C.M. / Robaire, S.A. / Ruccolo, S. / Schwalm, E.L. / Verma, D. / Xiao, L. / Selvaraj, B. / Zhang, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8tx5.cif.gz | 640 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8tx5.ent.gz | 419.1 KB | Display | PDB format |
PDBx/mmJSON format | 8tx5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8tx5_validation.pdf.gz | 468.5 KB | Display | wwPDB validaton report |
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Full document | 8tx5_full_validation.pdf.gz | 483.5 KB | Display | |
Data in XML | 8tx5_validation.xml.gz | 100.5 KB | Display | |
Data in CIF | 8tx5_validation.cif.gz | 149.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tx/8tx5 ftp://data.pdbj.org/pub/pdb/validation_reports/tx/8tx5 | HTTPS FTP |
-Related structure data
Related structure data | 8tx6C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 69532.555 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Fusarium graminearum (fungus) / Gene: GAOA / Production host: Escherichia coli (E. coli) / References: UniProt: P0CS93 #2: Chemical | ChemComp-CU / #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.94 Å3/Da / Density % sol: 58.11 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 10% vol PEG 3350, 200 mM Potassium monophosphate, 100 mM TRIS.HCl (pH 8.0) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 3, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→28.02 Å / Num. obs: 223522 / % possible obs: 92.7 % / Redundancy: 3.5 % / Biso Wilson estimate: 24.55 Å2 / CC1/2: 0.996 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 2.08→2.19 Å / Num. unique obs: 27814 / CC1/2: 0.81 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→28.02 Å / SU ML: 0.2144 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.6888 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.76 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.93→28.02 Å
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Refine LS restraints |
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LS refinement shell |
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