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Yorodumi- PDB-6a6r: Crystal structure of the modified fructosyl peptide oxidase from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6a6r | ||||||
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Title | Crystal structure of the modified fructosyl peptide oxidase from Aspergillus nidulans, Seleno-methionine Derivative | ||||||
Components | Fructosyl amine: oxygen oxidoreductase | ||||||
Keywords | OXIDOREDUCTASE / fructosyl peptide / Aspergillus nidulans / FAD-binding protein | ||||||
Function / homology | 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 / (4S,5S)-1,2-DITHIANE-4,5-DIOL / FLAVIN-ADENINE DINUCLEOTIDE Function and homology information | ||||||
Biological species | Aspergillus nidulans (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.609 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 | 6a6r.cif.gz | 180.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6a6r.ent.gz | 149.9 KB | Display | PDB format |
PDBx/mmJSON format | 6a6r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a6/6a6r ftp://data.pdbj.org/pub/pdb/validation_reports/a6/6a6r | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 49143.629 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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#2: Chemical | ChemComp-FAD / | ||||
#3: Chemical | #4: Chemical | ChemComp-SO4 / | #5: 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: 2.55 Å3/Da / Density % sol: 51.84 % Description: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns |
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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: SPring-8 / Beamline: BL38B1 / Wavelength: 0.9798 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 24, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9798 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 15887 / % possible obs: 100 % / Redundancy: 20 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 44.3 |
Reflection shell | Resolution: 2.6→2.64 Å / Rmerge(I) obs: 0.41 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.609→41.152 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.41 Details: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.609→41.152 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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