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- PDB-6ns2: Crystal structure of fungal lipoxygenase from Fusarium graminearu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ns2 | |||||||||
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Title | Crystal structure of fungal lipoxygenase from Fusarium graminearum. P212121 crystal form. | |||||||||
![]() | lipoxygenase | |||||||||
![]() | OXIDOREDUCTASE / lipoxygenase / fungus / Fe coordination | |||||||||
Function / homology | ![]() linoleate 11-lipoxygenase / linoleate 11-lipoxygenase activity / lipoxygenase pathway / arachidonic acid metabolic process / lipid oxidation / hepoxilin biosynthetic process / linoleic acid metabolic process / extracellular region / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Pakhomova, S. / Boeglin, W.E. / Neau, D.B. / Bartlett, S.G. / Brash, A.R. / Newcomer, M.E. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: An ensemble of lipoxygenase structures reveals novel conformations of the Fe coordination sphere. Authors: Pakhomova, S. / Boeglin, W.E. / Neau, D.B. / Bartlett, S.G. / Brash, A.R. / Newcomer, M.E. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 514.5 KB | Display | ![]() |
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PDB format | ![]() | 423.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 443 KB | Display | ![]() |
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Full document | ![]() | 451.2 KB | Display | |
Data in XML | ![]() | 42.7 KB | Display | |
Data in CIF | ![]() | 59 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ns3C ![]() 6ns4C ![]() 6ns5C ![]() 6ns6C ![]() 3rdeS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: _ / Auth seq-ID: 100 - 745 / Label seq-ID: 124 - 769
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Components
#1: Protein | Mass: 86406.766 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: PH-1 / ATCC MYA-4620 / FGSC 9075 / NRRL 31084 / Gene: FG02216.1, FGRAMPH1_01T05341 / Plasmid: pET-28b / Production host: ![]() ![]() References: UniProt: I1REW2, Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.22 % / Description: Plates |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 10% PEG3350, 0.05 M proline, 0.1 M imidazole acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 24, 2014 |
Radiation | Monochromator: Cryo-cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.7413 Å / Relative weight: 1 |
Reflection | Resolution: 2.79→47.58 Å / Num. obs: 40654 / % possible obs: 98.5 % / Redundancy: 6.2 % / Biso Wilson estimate: 31.6 Å2 / CC1/2: 0.993 / Rpim(I) all: 0.072 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 2.79→2.94 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 5781 / CC1/2: 0.828 / Rpim(I) all: 0.395 / % possible all: 97.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3RDE Resolution: 2.79→47.58 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.917 / SU B: 41.962 / SU ML: 0.347 / Cross valid method: THROUGHOUT / ESU R Free: 0.366 / 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: 57.842 Å2
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Refinement step | Cycle: 1 / Resolution: 2.79→47.58 Å
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Refine LS restraints |
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