+Open data
-Basic information
Entry | Database: PDB / ID: 6a0m | ||||||
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Title | Mandelate oxidase mutant-Y128F with 2-Phenylacetic 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 / : / fatty acid alpha-oxidation / L-lactate dehydrogenase activity / FMN binding / peroxisome / plasma membrane Similarity search - Function | ||||||
Biological species | Amycolatopsis orientalis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Li, T.L. / Lin, K.H. | ||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2019 Title: Biochemical and structural explorations of alpha-hydroxyacid oxidases reveal a four-electron oxidative decarboxylation reaction. Authors: Yeh, H.W. / Lin, K.H. / Lyu, S.Y. / 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 | 6a0m.cif.gz | 88.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6a0m.ent.gz | 64.4 KB | Display | PDB format |
PDBx/mmJSON format | 6a0m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6a0m_validation.pdf.gz | 786.9 KB | Display | wwPDB validaton report |
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Full document | 6a0m_full_validation.pdf.gz | 791.8 KB | Display | |
Data in XML | 6a0m_validation.xml.gz | 17.5 KB | Display | |
Data in CIF | 6a0m_validation.cif.gz | 26 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a0/6a0m ftp://data.pdbj.org/pub/pdb/validation_reports/a0/6a0m | HTTPS FTP |
-Related structure data
Related structure data | 5zzqC 5zzsC 5zzxC 5zzyC 6a00C 6a0dC 6a0gC 6a0oC 6a0yC 6a11C 6a1aC 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: 40029.562 Da / Num. of mol.: 1 / Mutation: Y128F 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-PAC / |
#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: 3.48 Å3/Da / Density % sol: 64.64 % |
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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: SPring-8 / Beamline: BL44XU / Wavelength: 1 Å |
Detector | Type: Bruker DIP-6040 / Detector: CCD / Date: Apr 23, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→30 Å / Num. obs: 54092 / % possible obs: 99.9 % / Redundancy: 9.3 % / Rmerge(I) obs: 0.037 / Rpim(I) all: 0.021 / Χ2: 0.944 / Net I/σ(I): 35.8 |
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 2 / Num. unique obs: 5363 / CC1/2: 0.768 / Rpim(I) all: 0.36 / Χ2: 0.838 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3SGZ Resolution: 1.75→30 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.896 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.08 / 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: 26.095 Å2
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Refinement step | Cycle: 1 / Resolution: 1.75→30 Å
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Refine LS restraints |
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