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Yorodumi- PDB-5t1f: Crystal structure of Phaeospaeria nodrum fructosyl peptide oxidas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5t1f | ||||||
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Title | Crystal structure of Phaeospaeria nodrum fructosyl peptide oxidase mutant Asn56Ala | ||||||
Components | Uncharacterized protein | ||||||
Keywords | OXIDOREDUCTASE / Fructosyl peptide oxidase / FAD | ||||||
Function / homology | Function and homology information saccharopine oxidase activity / sarcosine oxidase activity / flavin adenine dinucleotide binding Similarity search - Function | ||||||
Biological species | Phaeosphaeria nodorum | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å | ||||||
Authors | Yoshida, H. / Shimasaki, T. / Kamitori, S. / Sode, K. | ||||||
Citation | Journal: Sci Rep / Year: 2017 Title: X-ray structures of fructosyl peptide oxidases revealing residues responsible for gating oxygen access in the oxidative half reaction Authors: Shimasaki, T. / Yoshida, H. / Kamitori, S. / Sode, K. #1: Journal: Biotechnol. Bioeng. / Year: 2010 Title: Motif-based search for a novel fructosyl peptide oxidase from genome databases. Authors: Kim, S. / Ferri, S. / Tsugawa, W. / Mori, K. / Sode, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5t1f.cif.gz | 105.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5t1f.ent.gz | 77.5 KB | Display | PDB format |
PDBx/mmJSON format | 5t1f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t1/5t1f ftp://data.pdbj.org/pub/pdb/validation_reports/t1/5t1f | HTTPS FTP |
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-Related structure data
Related structure data | 5t1eSC 5xaoC 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
#1: Protein | Mass: 49057.516 Da / Num. of mol.: 1 / Mutation: N56A Source method: isolated from a genetically manipulated source Details: N56A mutant Source: (gene. exp.) Phaeosphaeria nodorum (strain SN15 / ATCC MYA-4574 / FGSC 10173) (fungus) Strain: SN15 / ATCC MYA-4574 / FGSC 10173 / Gene: SNOG_08398 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q0UIL6 |
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#2: Chemical | ChemComp-FAD / |
#3: Chemical | ChemComp-ACY / |
#4: 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: 1.96 Å3/Da / Density % sol: 37.14 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 8%(w/v) Tacsimate, 18-22%(w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 2, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→50 Å / Num. obs: 24157 / % possible obs: 91.9 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 1.98→2.01 Å / Redundancy: 3 % / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 2 / % possible all: 84.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5T1E Resolution: 1.98→39.14 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.957 / SU B: 4.146 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.214 / ESU R Free: 0.161 / 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: 32.53 Å2
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Refinement step | Cycle: LAST / Resolution: 1.98→39.14 Å
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Refine LS restraints |
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