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Yorodumi- PDB-6a6u: Crystal structure of the modified fructosyl peptide oxidase from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6a6u | |||||||||
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Title | Crystal structure of the modified fructosyl peptide oxidase from Aspergillus nidulans with R61G mutation, in complex with FSA | |||||||||
Components | Fructosyl amine: oxygen oxidoreductase | |||||||||
Keywords | OXIDOREDUCTASE / fructosyl peptide / Aspergillus nidulans / FAD-binding protein | |||||||||
Function / homology | Function and homology information D-Amino Acid Oxidase, subunit A, domain 2 / D-Amino Acid Oxidase; Chain A, domain 2 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / 2-Layer Sandwich / Alpha Beta Similarity search - Domain/homology | |||||||||
Biological species | Aspergillus nidulans (mold) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.945 Å | |||||||||
Authors | Ogawa, N. / Maruyama, Y. / Itoh, T. / Hashimoto, W. / Murata, K. | |||||||||
Citation | Journal: Sci Rep / Year: 2019 Title: Creation of haemoglobin A1c direct oxidase from fructosyl peptide oxidase by combined structure-based site specific mutagenesis and random mutagenesis. Authors: Ogawa, N. / Kimura, T. / Umehara, F. / Katayama, Y. / Nagai, G. / Suzuki, K. / Aisaka, K. / Maruyama, Y. / Itoh, T. / Hashimoto, W. / Murata, K. / Ichimura, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6a6u.cif.gz | 191.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6a6u.ent.gz | 149.1 KB | Display | PDB format |
PDBx/mmJSON format | 6a6u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a6/6a6u ftp://data.pdbj.org/pub/pdb/validation_reports/a6/6a6u | HTTPS FTP |
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-Related structure data
Related structure data | 6a6rSC 6a6sC 6a6tC 6a6vC 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 on special symmetry positions |
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-Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 48621.438 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus nidulans (mold) / Production host: Escherichia coli (E. coli) |
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#3: Sugar | ChemComp-FSA / |
-Non-polymers , 4 types, 291 molecules
#2: Chemical | ChemComp-FAD / | ||||
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#4: Chemical | ChemComp-D1D / ( #5: Chemical | #6: 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: 2.53 Å3/Da / Density % sol: 51.32 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 10.4 Details: 1.75 M ammonium sulfate, 0.2 M lithium sulfate, 0.08 M CAPS (N-cyclohexyl-3-aminopropanesulfonic acid) buffer (pH 10.4) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 12, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.945→50 Å / Num. obs: 36930 / % possible obs: 99.8 % / Redundancy: 10.3 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 44.2 |
Reflection shell | Resolution: 1.95→1.98 Å / Rmerge(I) obs: 0.461 / Num. unique obs: 1828 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6A6R Resolution: 1.945→40.755 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.86
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.945→40.755 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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