+Open data
-Basic information
Entry | Database: PDB / ID: 6ai7 | ||||||
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Title | Mandelate oxidase mutant-Y128F with the C4a-OH-FMN adduct | ||||||
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 / peroxisome / FMN binding / plasma membrane Similarity search - Function | ||||||
Biological species | Amycolatopsis orientalis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å | ||||||
Authors | Li, T.L. / Lin, K.H. | ||||||
Citation | Journal: To Be Published Title: The crystal structure of Mandelate oxidase mutant-Y128F with the C4a-OH-FMN adduct Authors: Li, T.L. / Lin, K.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ai7.cif.gz | 81.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ai7.ent.gz | 59.7 KB | Display | PDB format |
PDBx/mmJSON format | 6ai7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ai7_validation.pdf.gz | 750.8 KB | Display | wwPDB validaton report |
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Full document | 6ai7_full_validation.pdf.gz | 758.7 KB | Display | |
Data in XML | 6ai7_validation.xml.gz | 15.4 KB | Display | |
Data in CIF | 6ai7_validation.cif.gz | 21.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ai/6ai7 ftp://data.pdbj.org/pub/pdb/validation_reports/ai/6ai7 | HTTPS FTP |
-Related structure data
Related structure data | 3sgzS S: Starting model for refinement |
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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: 38140.473 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-9Q6 / |
#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: 3.4 Å3/Da / Density % sol: 63.77 % |
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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 20, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.07→30 Å / Num. obs: 32246 / % possible obs: 100 % / Redundancy: 9.3 % / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.024 / Χ2: 0.924 / Net I/σ(I): 30.2 |
Reflection shell | Resolution: 2.07→2.14 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 3167 / CC1/2: 0.911 / Rpim(I) all: 0.22 / Χ2: 0.809 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3SGZ Resolution: 2.07→30 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.914 / SU B: 3.903 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.157 / 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: 33.796 Å2
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Refinement step | Cycle: 1 / Resolution: 2.07→30 Å
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Refine LS restraints |
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