+Open data
-Basic information
Entry | Database: PDB / ID: 7f21 | |||||||||
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Title | L-lactate oxidase with D-lactate | |||||||||
Components | L-lactate oxidase | |||||||||
Keywords | OXIDOREDUCTASE / D-lactate / complex | |||||||||
Function / homology | FLAVIN MONONUCLEOTIDE / LACTIC ACID Function and homology information | |||||||||
Biological species | Aerococcus viridans (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å | |||||||||
Authors | Morimoto, Y. / Inaka, K. | |||||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2021 Title: Dynamic interactions in the l-lactate oxidase active site facilitate substrate binding at pH4.5. Authors: Furubayashi, N. / Inaka, K. / Kamo, M. / Umena, Y. / Matsuoka, T. / Morimoto, Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7f21.cif.gz | 185.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7f21.ent.gz | 137.9 KB | Display | PDB format |
PDBx/mmJSON format | 7f21.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f2/7f21 ftp://data.pdbj.org/pub/pdb/validation_reports/f2/7f21 | HTTPS FTP |
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-Related structure data
Related structure data | 7f1yC 7f20C 7f22C 2du2S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: 78793.289 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aerococcus viridans (bacteria) / Production host: Aerococcus viridans (bacteria) #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.29 Å3/Da / Density % sol: 4.47 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion Details: 20 mg/ml in 50 mM sodium acetate (pH4.5) , 40% ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 20, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.38→46.99 Å / Num. obs: 155462 / % possible obs: 99.37 % / Redundancy: 16.6 % / CC1/2: 0.96 / Net I/σ(I): 11.65 |
Reflection shell | Resolution: 1.38→1.429 Å / Num. unique obs: 16056 / CC1/2: 0.56 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2DU2 Resolution: 1.38→46.99 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.598 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.001 Å2
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Refinement step | Cycle: 1 / Resolution: 1.38→46.99 Å
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Refine LS restraints |
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