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Open data
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Basic information
Entry | Database: PDB / ID: 1lnh | ||||||
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Title | LIPOXYGENASE-3(SOYBEAN) NON-HEME FE(II) METALLOPROTEIN | ||||||
![]() | LIPOXYGENASE-3 | ||||||
![]() | OXIDOREDUCTASE / METALLOPROTEIN / FE(II) COMPLEX | ||||||
Function / homology | ![]() linoleate 9S-lipoxygenase / linoleate 9S-lipoxygenase activity / oxylipin biosynthetic process / lipid oxidation / 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 | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Skrzypczak-Jankun, E. | ||||||
![]() | ![]() Title: Structure of soybean lipoxygenase L3 and a comparison with its L1 isoenzyme. Authors: Skrzypczak-Jankun, E. / Amzel, L.M. / Kroa, B.A. / Funk Jr., M.O. #1: ![]() Title: Lipoxygenase-A Molecular Complex with a Non-Heme Iron Authors: Skrzypczak-Jankun, E. / Funk Junior, M.O. / Boyington, J.C. / Amzel, L.M. #2: ![]() Title: Position 713 is Critical for Catalysis But not Iron Binding in Soybean Lipoxygenase 3 Authors: Kramer, J.A. / Johnson, K.R. / Dunham, W.R. / Sands, R.H. / Funk Junior, M.O. #3: ![]() Title: Crystallization and Preliminary X-Ray Characterization of a Soybean Seed Lipoxygenase Authors: Stallings, W.C. / Kroa, B.A. / Carroll, R.T. / Metzger, A.L. / Funk, M.O. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 183 KB | Display | ![]() |
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PDB format | ![]() | 142.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 434.4 KB | Display | ![]() |
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Full document | ![]() | 478.2 KB | Display | |
Data in XML | ![]() | 36.4 KB | Display | |
Data in CIF | ![]() | 50.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 96919.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: Chemical | ChemComp-FE2 / |
#3: Water | ChemComp-HOH / |
Compound details | THE NUMBERING OF THE SECONDARY STRUCTURE ELEMENTS HAS SYMBOLS AFTER SOYBEAN LIPOXYGENASE L1 AS IN ...THE NUMBERING OF THE SECONDARY STRUCTURE ELEMENTS HAS SYMBOLS AFTER SOYBEAN LIPOXYGENA |
Nonpolymer details | THE IRON BINDING SITE CONSISTS OF HIS 518, HIS 523, HIS 709 AND ILE 857(C-TERMINAL) THAT ARE ...THE IRON BINDING SITE CONSISTS OF HIS 518, HIS 523, HIS 709 AND ILE 857(C-TERMINAL) THAT ARE COVALENTLY |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.3 / Details: pH 5.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 23 ℃ / Method: vapor diffusion, sitting drop | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 296 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: 1994 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→61.6 Å / Num. obs: 23403 / % possible obs: 80.1 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.062 |
Reflection shell | Resolution: 2.6→2.75 Å / Rmerge(I) obs: 0.117 / Mean I/σ(I) obs: 3.39 / % possible all: 43.6 |
Reflection | *PLUS Num. measured all: 74331 |
Reflection shell | *PLUS % possible obs: 48 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: FOR MOLECULAR REPLACEMENT: 1SBL FOR SOYBEAN LIPOXYGENASE-1. THE MODEL WAS TRUNCATED TO INCLUDE ONLY THE ATOMS (7854) COMMON WITH LIPOXYGENASE-3 SEQUENCE (ENTRY 1SBL WAS REPLACED LATER ...Starting model: FOR MOLECULAR REPLACEMENT: 1SBL FOR SOYBEAN LIPOXYGENASE-1. THE MODEL WAS TRUNCATED TO INCLUDE ONLY THE ATOMS (7854) COMMON WITH LIPOXYGENASE-3 SEQUENCE (ENTRY 1SBL WAS REPLACED LATER IN PDB BY 2SBL WITH BETTER REFINED MODEL). Resolution: 2.6→8 Å / σ(F): 2
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Displacement parameters | Biso mean: 31.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→8 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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