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Yorodumi- PDB-6iwe: Crystal structure of fructosyl peptide oxidase thermally stable mutant -
+Open data
-Basic information
Entry | Database: PDB / ID: 6iwe | ||||||
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Title | Crystal structure of fructosyl peptide oxidase thermally stable mutant | ||||||
Components | Fructosyl peptide oxidase | ||||||
Keywords | OXIDOREDUCTASE / fructosyl peptide oxidase / thermal mutant | ||||||
Function / homology | Function and homology information Oxidoreductases; Acting on the CH-NH group of donors; With oxygen as acceptor / flavin adenine dinucleotide binding / oxidoreductase activity Similarity search - Function | ||||||
Biological species | Penicillium terrenum (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.939 Å | ||||||
Authors | Fuqing, M. / Guangyu, Y. | ||||||
Citation | Journal: To Be Published Title: crystal structure of fructosyl peptide oxidase thermally stable mutant Authors: Fuqiang, M. / Guangyu, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6iwe.cif.gz | 181.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6iwe.ent.gz | 143.3 KB | Display | PDB format |
PDBx/mmJSON format | 6iwe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6iwe_validation.pdf.gz | 700.6 KB | Display | wwPDB validaton report |
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Full document | 6iwe_full_validation.pdf.gz | 702.8 KB | Display | |
Data in XML | 6iwe_validation.xml.gz | 17.2 KB | Display | |
Data in CIF | 6iwe_validation.cif.gz | 23.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iw/6iwe ftp://data.pdbj.org/pub/pdb/validation_reports/iw/6iwe | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 48476.113 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Penicillium terrenum (fungus) / Gene: fpoxE / Production host: Escherichia coli (E. coli) References: UniProt: Q765A9, Oxidoreductases; Acting on the CH-NH group of donors; With oxygen as acceptor |
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#2: Chemical | ChemComp-FAD / |
#3: 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: 2.5 Å3/Da / Density % sol: 50.79 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 0.2M potassium phosphate dibasic, 20%(w/v) polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 8, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→47.52 Å / Num. obs: 36666 / % possible obs: 100 % / Redundancy: 5.06 % / Net I/σ(I): 16 |
Reflection shell | Resolution: 1.97→2 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.939→47.54 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.38 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.939→47.54 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -23.3763 Å / Origin y: 33.4423 Å / Origin z: 19.8214 Å
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Refinement TLS group | Selection details: all |