+Open data
-Basic information
Entry | Database: PDB / ID: 7soi | ||||||
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Title | Structure of I552A Soybean Lipoxygenase at 277K | ||||||
Components | Lipoxygenase | ||||||
Keywords | OXIDOREDUCTASE / metal binding / lipid binding | ||||||
Function / homology | Function and homology information Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen / oxylipin biosynthetic process / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / fatty acid biosynthetic process / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Glycine max (soybean) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å | ||||||
Authors | Gee, C.L. / Offenbacher, A.R. / Hu, S. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2023 Title: Temporal and spatial resolution of distal protein motions that activate hydrogen tunneling in soybean lipoxygenase. Authors: Zaragoza, J.P.T. / Offenbacher, A.R. / Hu, S. / Gee, C.L. / Firestein, Z.M. / Minnetian, N. / Deng, Z. / Fan, F. / Iavarone, A.T. / Klinman, J.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7soi.cif.gz | 788.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7soi.ent.gz | 532.9 KB | Display | PDB format |
PDBx/mmJSON format | 7soi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/so/7soi ftp://data.pdbj.org/pub/pdb/validation_reports/so/7soi | HTTPS FTP |
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-Related structure data
Related structure data | 7sojC 5t5vS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 94480.078 Da / Num. of mol.: 2 / Mutation: I552A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Glycine max (soybean) / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: B3TDK4, Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen #2: Chemical | #3: Chemical | ChemComp-NA / | #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: 2.24 Å3/Da / Density % sol: 45.05 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 9% PEG3350, 200 mM sodium acetate, pH 5.5 |
-Data collection
Diffraction | Mean temperature: 277 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.88557 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 19, 2017 |
Radiation | Monochromator: S111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.88557 Å / Relative weight: 1 |
Reflection | Resolution: 2→46.38 Å / Num. obs: 109110 / % possible obs: 97 % / Redundancy: 5.4 % / Biso Wilson estimate: 33.21 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.254 / Rpim(I) all: 0.183 / Rrim(I) all: 0.314 / Net I/σ(I): 4.2 |
Reflection shell | Resolution: 2→2.03 Å / Rmerge(I) obs: 4.78 / Num. unique obs: 4240 / CC1/2: 0.105 / Rpim(I) all: 3.98 / % possible all: 75.7 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 5t5v Resolution: 2→46.38 Å / SU ML: 0.3522 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.253 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.2 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→46.38 Å
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Refine LS restraints |
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LS refinement shell |
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