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Yorodumi- PDB-4qwt: Anaerobic crystal structure of delta413-417:GS LOX in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4qwt | ||||||
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Title | Anaerobic crystal structure of delta413-417:GS LOX in complex with arachidonate | ||||||
Components | Allene oxide synthase-lipoxygenase protein | ||||||
Keywords | OXIDOREDUCTASE / iron binding / membrane-associated | ||||||
Function / homology | Function and homology information arachidonate 8-lipoxygenase / arachidonate 8(R)-lipoxygenase activity / allene oxide synthase activity / lipoxygenase pathway / Lyases; Carbon-oxygen lyases; Hydro-lyases / oxylipin biosynthetic process / arachidonic acid metabolic process / lipid oxidation / hepoxilin biosynthetic process / linoleic acid metabolic process ...arachidonate 8-lipoxygenase / arachidonate 8(R)-lipoxygenase activity / allene oxide synthase activity / lipoxygenase pathway / Lyases; Carbon-oxygen lyases; Hydro-lyases / oxylipin biosynthetic process / arachidonic acid 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 / MOLECULAR REPLACEMENT / Resolution: 2.002 Å | ||||||
Authors | Neau, D.B. / Newcomer, M.E. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 Title: Crystal Structure of a Lipoxygenase in Complex with Substrate: THE ARACHIDONIC ACID-BINDING SITE OF 8R-LIPOXYGENASE. Authors: Neau, D.B. / Bender, G. / Boeglin, W.E. / Bartlett, S.G. / Brash, A.R. / 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 | 4qwt.cif.gz | 602.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qwt.ent.gz | 493.7 KB | Display | PDB format |
PDBx/mmJSON format | 4qwt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4qwt_validation.pdf.gz | 740.5 KB | Display | wwPDB validaton report |
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Full document | 4qwt_full_validation.pdf.gz | 755.3 KB | Display | |
Data in XML | 4qwt_validation.xml.gz | 116.7 KB | Display | |
Data in CIF | 4qwt_validation.cif.gz | 166.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qw/4qwt ftp://data.pdbj.org/pub/pdb/validation_reports/qw/4qwt | HTTPS FTP |
-Related structure data
Related structure data | 3gf1S 3fgi S: Starting model for refinement |
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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: 79408.992 Da / Num. of mol.: 4 / Fragment: lipoxygenase domain (UNP residues 374-1066) / Mutation: delta413-417:GS Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plexaura homomalla (black sea rod) / Plasmid: pET3a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O16025, arachidonate 8-lipoxygenase |
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-Non-polymers , 7 types, 1856 molecules
#2: Chemical | ChemComp-FE2 / #3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-ACT / #5: Chemical | ChemComp-GOL / #6: Chemical | ChemComp-CL / #7: Chemical | ChemComp-ACD / | #8: Water | ChemComp-HOH / | |
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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: 2.91 Å3/Da / Density % sol: 57.79 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 6-8% PEG8000, 5% glycerol, 0.2 M calcium chloride, 0.1 M imidazole acetate, pH 8.0, anaerobic, temperature 298K, VAPOR DIFFUSION, SITTING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 14, 2010 / Details: mirrors |
Radiation | Monochromator: Cryogenically-cooled single crystal Si(220) side bounce Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 243605 / Num. obs: 242387 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.102 / Rsym value: 0.119 / Net I/σ(I): 11.68 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.813 / Mean I/σ(I) obs: 1.9 / Rsym value: 0.951 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3GF1 Resolution: 2.002→48.416 Å / SU ML: 0.24 / Isotropic thermal model: ISOTROPIC / σ(F): 1.34 / Phase error: 22.11 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.32 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.002→48.416 Å
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Refine LS restraints |
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LS refinement shell |
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