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- PDB-4g32: Crystal Structure of a Phospholipid-Lipoxygenase Complex from Pse... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4g32 | ||||||
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Title | Crystal Structure of a Phospholipid-Lipoxygenase Complex from Pseudomonas aeruginosa at 1.75A (P21212) | ||||||
![]() | 15S-LIPOXYGENASE | ||||||
![]() | OXIDOREDUCTASE / Non-heme iron enzyme / Protein-phospholipid complex | ||||||
Function / homology | ![]() oleate 10S-lipoxygenase / linoleate 9S-lipoxygenase / linoleate 9S-lipoxygenase activity / linoleate 13S-lipoxygenase / linoleate 13S-lipoxygenase activity / lipoxygenase pathway / arachidonic acid metabolic process / lipid oxidation / hepoxilin biosynthetic process / linoleic acid metabolic process ...oleate 10S-lipoxygenase / linoleate 9S-lipoxygenase / linoleate 9S-lipoxygenase activity / linoleate 13S-lipoxygenase / linoleate 13S-lipoxygenase activity / lipoxygenase pathway / arachidonic acid metabolic process / lipid oxidation / hepoxilin biosynthetic process / linoleic acid metabolic process / periplasmic space / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Carpena, X. / Garreta, A. / Val-Moraes, S.P. / Garcia-Fernandez, Q. / Fita, I. | ||||||
![]() | ![]() Title: Structure and interaction with phospholipids of a prokaryotic lipoxygenase from Pseudomonas aeruginosa. Authors: Garreta, A. / Val-Moraes, S.P. / Garcia-Fernandez, Q. / Busquets, M. / Juan, C. / Oliver, A. / Ortiz, A. / Gaffney, B.J. / Fita, I. / Manresa, A. / Carpena, X. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 157.8 KB | Display | ![]() |
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PDB format | ![]() | 117.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 759.5 KB | Display | ![]() |
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Full document | ![]() | 766.1 KB | Display | |
Data in XML | ![]() | 31 KB | Display | |
Data in CIF | ![]() | 48.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4g33C ![]() 2fnqS 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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Components
#1: Protein | Mass: 75053.500 Da / Num. of mol.: 1 Fragment: Secretable Pa_LOX without the periplasmic signal peptide Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q8RNT4, Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen | ||||
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#2: Chemical | ChemComp-FE2 / | ||||
#3: Chemical | ChemComp-ZPE / ( | ||||
#4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | Nonpolymer details | PHOSPHATIDYLETHANOLAMINE PHOSPHOLIPID HAS FATTY ACID CHAINS OF 18 (SN1) AND 14/16 (SN2) CARBON ...PHOSPHATID | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.83 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 10% PEG 3350, 50mM magnesium chloride, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9334 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→20 Å / Num. all: 66015 / Num. obs: 66015 / % possible obs: 97.9 % / Redundancy: 3.9 % / Rsym value: 0.093 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 3.5 % / Rsym value: 0.63 / % possible all: 97 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2FNQ (498-1066) Resolution: 1.75→20 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.847 / SU ML: 0.082 / SU R Cruickshank DPI: 0.156 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.115 / 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: 22.535 Å2
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Refine analyze | Luzzati coordinate error obs: 0.204 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→20 Å
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Refine LS restraints |
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