+Open data
-Basic information
Entry | Database: PDB / ID: 6a1a | ||||||
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Title | Mandelate oxidase mutant-Y128F with 4-hydroxymandelic 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: 1.35 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 | 6a1a.cif.gz | 93.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6a1a.ent.gz | 67.6 KB | Display | PDB format |
PDBx/mmJSON format | 6a1a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6a1a_validation.pdf.gz | 786.6 KB | Display | wwPDB validaton report |
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Full document | 6a1a_full_validation.pdf.gz | 790.5 KB | Display | |
Data in XML | 6a1a_validation.xml.gz | 18.8 KB | Display | |
Data in CIF | 6a1a_validation.cif.gz | 29.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a1/6a1a ftp://data.pdbj.org/pub/pdb/validation_reports/a1/6a1a | HTTPS FTP |
-Related structure data
Related structure data | 5zzqC 5zzsC 5zzxC 5zzyC 6a00C 6a0dC 6a0gC 6a0mC 6a0oC 6a0yC 6a11C 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 | #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: 3.5 Å3/Da / Density % sol: 64.82 % |
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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: Jul 8, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→30 Å / Num. obs: 116144 / % possible obs: 100 % / Redundancy: 12.2 % / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.02 / Χ2: 0.95 / Net I/σ(I): 36.09 |
Reflection shell | Resolution: 1.35→1.4 Å / Redundancy: 12 % / Rmerge(I) obs: 0.746 / Mean I/σ(I) obs: 2.69 / Num. unique obs: 11478 / CC1/2: 0.844 / Rpim(I) all: 0.269 / Χ2: 0.824 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3SGZ Resolution: 1.35→30 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.968 / SU B: 0.68 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.042 / ESU R Free: 0.043 / 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: 17.726 Å2
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Refinement step | Cycle: 1 / Resolution: 1.35→30 Å
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Refine LS restraints |
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