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Yorodumi- PDB-5zzz: The crystal structure of Mandelate oxidase Y128C with benzoyl-for... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5zzz | ||||||
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Title | The crystal structure of Mandelate oxidase Y128C with benzoyl-formic acid | ||||||
Components | 4-hydroxymandelate oxidase | ||||||
Keywords | FLAVOPROTEIN / FMN-dependent oxidase | ||||||
Function / homology | Function and homology information 4-hydroxymandelate oxidase / oxidoreductase activity, acting on the CH-OH group of donors, oxygen as acceptor / vancomycin biosynthetic process / FMN binding Similarity search - Function | ||||||
Biological species | Amycolatopsis orientalis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.446 Å | ||||||
Authors | Li, T.L. / Lin, K.H. | ||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2019 Title: The flavin mononucleotide cofactor in alpha-hydroxyacid oxidases exerts its electrophilic/nucleophilic duality in control of the substrate-oxidation level. Authors: Lyu, S.Y. / Lin, K.H. / Yeh, H.W. / Li, Y.S. / Huang, C.M. / Wang, Y.L. / Shih, H.W. / Hsu, N.S. / Wu, C.J. / Li, T.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zzz.cif.gz | 89.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zzz.ent.gz | 63.3 KB | Display | PDB format |
PDBx/mmJSON format | 5zzz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zz/5zzz ftp://data.pdbj.org/pub/pdb/validation_reports/zz/5zzz | HTTPS FTP |
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-Related structure data
Related structure data | 5zzpC 5zzrC 6a08C 6a0vC 6a13C 6a19C 6a1hC 6a1lC 6a1mC 6a1pC 6a1rC 6a21C 6a23C 6a3tC 3sgzS 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: 40001.531 Da / Num. of mol.: 1 / Mutation: Y128C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Amycolatopsis orientalis (bacteria) / Gene: hmo / Production host: Escherichia coli (E. coli) / References: UniProt: O52792, 4-hydroxymandelate oxidase |
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#2: Chemical | ChemComp-FMN / |
#3: Chemical | ChemComp-173 / |
#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: 3.51 Å3/Da / Density % sol: 64.99 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 35% Tascimate, 0.1M Bis-Tris propane pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Oct 6, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.446→30 Å / Num. obs: 95971 / % possible obs: 99.9 % / Redundancy: 9.9 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 33.5 |
Reflection shell | Resolution: 1.446→1.5 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.754 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 9495 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3SGZ Resolution: 1.446→27.109 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.27
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.446→27.109 Å
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Refine LS restraints |
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LS refinement shell |
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