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- PDB-6ns4: Crystal structure of fungal lipoxygenase from Fusarium graminearu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ns4 | |||||||||
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Title | Crystal structure of fungal lipoxygenase from Fusarium graminearum. C2 crystal form. | |||||||||
![]() | lipoxygenase | |||||||||
![]() | OXIDOREDUCTASE / lipoxygenase / fungus / Fe coordination | |||||||||
Function / homology | ![]() linoleate 11-lipoxygenase / linoleate 11-lipoxygenase activity / lipoxygenase pathway / arachidonate metabolic process / lipid oxidation / hepoxilin biosynthetic process / linoleic acid metabolic process / 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 | ![]() | 543.3 KB | Display | ![]() |
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PDB format | ![]() | 445.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6ns2C ![]() 6ns3C ![]() 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: THR / End label comp-ID: THR / Refine code: _ / Auth seq-ID: 9 - 739 / Label seq-ID: 33 - 763
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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: Chemical | ChemComp-ACT / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 42 % / Description: cluster of plates |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.46 / Details: 25% PEG3350, 0.3 M ammonium acetate, 0.1 M HEPES |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Nov 16, 2016 / Details: MIRRORS |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.38079 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→40 Å / Num. obs: 55511 / % possible obs: 99.7 % / Redundancy: 3.7 % / Biso Wilson estimate: 20.4 Å2 / Rpim(I) all: 0.083 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 5447 / CC1/2: 0.71 / Rpim(I) all: 0.359 / % possible all: 97.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3RDE Resolution: 2.4→35.4 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.914 / SU B: 18.028 / SU ML: 0.204 / Cross valid method: THROUGHOUT / ESU R: 0.487 / ESU R Free: 0.241 / 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: 31.878 Å2
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Refinement step | Cycle: 1 / Resolution: 2.4→35.4 Å
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Refine LS restraints |
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