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Yorodumi- PDB-6r9v: Crystal structure of Pediococcus acidilactici lactate oxidase A94... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6r9v | ||||||
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Title | Crystal structure of Pediococcus acidilactici lactate oxidase A94G mutant | ||||||
Components | Putative L-lactate oxidase | ||||||
Keywords | OXIDOREDUCTASE / TIM Barrel / FMN / alpha hydroxyacid. | ||||||
Function / homology | Function and homology information : / fatty acid alpha-oxidation / L-lactate dehydrogenase activity / FMN binding / peroxisome / plasma membrane Similarity search - Function | ||||||
Biological species | Pediococcus acidilactici DSM 20284 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Ashok, Y. / Maksimainen, M.M. / Lehtio, L. | ||||||
Funding support | Finland, 1items
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Citation | Journal: Plos One / Year: 2020 Title: FMN-dependent oligomerization of putative lactate oxidase from Pediococcus acidilactici. Authors: Ashok, Y. / Maksimainen, M.M. / Kallio, T. / Kilpelainen, P. / Lehtio, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6r9v.cif.gz | 92.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6r9v.ent.gz | 67.7 KB | Display | PDB format |
PDBx/mmJSON format | 6r9v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r9/6r9v ftp://data.pdbj.org/pub/pdb/validation_reports/r9/6r9v | HTTPS FTP |
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-Related structure data
Related structure data | 6rhsC 6rhtC 2j6xS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 39704.750 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pediococcus acidilactici DSM 20284 (bacteria) Gene: lctO, HMPREF0623_0568 / Production host: Escherichia coli (E. coli) / References: UniProt: E0NE46, EC: 1.1.99.- | ||
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#2: Chemical | ChemComp-FMN / | ||
#3: Chemical | ChemComp-PG4 / | ||
#4: Chemical | #5: 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: 3.45 Å3/Da / Density % sol: 64.4 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 1.1M Sodium Malonate, 0.1M Hepes pH 7.0, 0.5% Jeffamine ED-2003. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 14, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 39425 / % possible obs: 100 % / Redundancy: 13.2 % / Net I/σ(I): 11.98 |
Reflection shell | Resolution: 2→2.05 Å / Num. unique obs: 2879 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2J6X Resolution: 2→45.92 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.994 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.102 / 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: 24.29 Å2
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Refinement step | Cycle: 1 / Resolution: 2→45.92 Å
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Refine LS restraints |
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