+Open data
-Basic information
Entry | Database: PDB / ID: 3fg4 | ||||||
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Title | Crystal structure of Delta413-417:GS I805A LOX | ||||||
Components | Allene oxide synthase-lipoxygenase protein | ||||||
Keywords | OXIDOREDUCTASE / lipoxygenase / arichidonic metabolism / Dioxygenase / Fatty acid biosynthesis / Heme / Iron / Lipid synthesis / Lyase / Membrane / Metal-binding / Multifunctional enzyme / Oxylipin biosynthesis | ||||||
Function / homology | Function and homology information arachidonate 8-lipoxygenase / arachidonate 8(R)-lipoxygenase activity / allene oxide synthase activity / Lyases; Carbon-oxygen lyases; Hydro-lyases / oxylipin biosynthetic process / lipoxygenase pathway / arachidonate metabolic process / lipid oxidation / hepoxilin biosynthetic process / linoleic acid metabolic process ...arachidonate 8-lipoxygenase / arachidonate 8(R)-lipoxygenase activity / allene oxide synthase activity / Lyases; Carbon-oxygen lyases; Hydro-lyases / oxylipin biosynthetic process / lipoxygenase pathway / arachidonate metabolic process / lipid oxidation / hepoxilin biosynthetic process / linoleic acid metabolic process / iron ion binding / heme binding / membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Plexaura homomalla (black sea rod) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.31 Å | ||||||
Authors | Neau, D.B. / Newcomer, M.E. | ||||||
Citation | Journal: Biochemistry / Year: 2009 Title: The 1.85 A structure of an 8R-lipoxygenase suggests a general model for lipoxygenase product specificity. Authors: Neau, D.B. / Gilbert, N.C. / Bartlett, S.G. / Boeglin, W. / Brash, A.R. / Newcomer, M.E. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2007 Title: Improving protein crystal quality by selective removal of a Ca(2+)-dependent membrane-insertion loop. Authors: Neau, D.B. / Gilbert, N.C. / Bartlett, S.G. / Dassey, A. / Newcomer, M.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fg4.cif.gz | 588.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fg4.ent.gz | 478 KB | Display | PDB format |
PDBx/mmJSON format | 3fg4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3fg4_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 3fg4_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 3fg4_validation.xml.gz | 114.7 KB | Display | |
Data in CIF | 3fg4_validation.cif.gz | 166.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fg/3fg4 ftp://data.pdbj.org/pub/pdb/validation_reports/fg/3fg4 | HTTPS FTP |
-Related structure data
Related structure data | 3fg1SC 3fg3C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 79366.914 Da / Num. of mol.: 4 Fragment: Arachidonate 8R-lipoxygenase: UNP residues 374-1066 Mutation: delta 413-417:GS, I805A Source method: isolated from a genetically manipulated source Details: lipoxygenase portion of an allen-oxide synthase/lipoxygenase fusion protein, expressed with an N-terminal His-Tag. Source: (gene. exp.) Plexaura homomalla (black sea rod) / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O16025, arachidonate 8-lipoxygenase |
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-Non-polymers , 7 types, 1642 molecules
#2: Chemical | ChemComp-FE2 / #3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-ACD / #5: Chemical | ChemComp-ACY / #6: Chemical | ChemComp-GOL / #7: Chemical | ChemComp-CL / #8: Water | ChemComp-HOH / | |
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-Details
Sequence details | AUTHORS CLEARLY SEE ISOLEUCINES IN ELECTRON DENSITY INSTEAD OF VALINES PROVIDED IN THE DATABASE ...AUTHORS CLEARLY SEE ISOLEUCINE |
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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: 2.92 Å3/Da / Density % sol: 57.94 % |
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Crystal grow | Temperature: 298 K / pH: 8 Details: 6-8% PEG 8000, 5% Glycerol, 0.2M CaCl2, 0.1M Imidazole acetate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CAMD / Beamline: GCPCC / Wavelength: 1.38 |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: May 30, 2008 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.38 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30.03 Å / Num. obs: 158438 / % possible obs: 100 % / Redundancy: 4.9 % / Biso Wilson estimate: 34.9 Å2 / Rmerge(I) obs: 0.124 / Net I/σ(I): 12.818 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.66 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 3FG1 Resolution: 2.31→30.03 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.912 / Occupancy max: 1 / Occupancy min: 0.15 / SU B: 6.031 / SU ML: 0.148 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.257 / ESU R Free: 0.223 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.22 Å2
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Refinement step | Cycle: LAST / Resolution: 2.31→30.03 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.31→2.37 Å / Total num. of bins used: 20
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