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Yorodumi- PDB-1hu9: LIPOXYGENASE-3 (SOYBEAN) COMPLEX WITH 4-HYDROPEROXY-2-METHOXY-PHENOL -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hu9 | ||||||
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Title | LIPOXYGENASE-3 (SOYBEAN) COMPLEX WITH 4-HYDROPEROXY-2-METHOXY-PHENOL | ||||||
Components | LIPOXYGENASE-3 | ||||||
Keywords | OXIDOREDUCTASE / METALLOPROTEIN / FE(III) COMPLEX / PURPLE LIPOXYGENASE / ENZYME INHIBITOR | ||||||
Function / homology | Function and homology information linoleate 9S-lipoxygenase / linoleate 9S-lipoxygenase activity / oxylipin biosynthetic process / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / lipid oxidation / fatty acid biosynthetic process / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Glycine max (soybean) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Zhou, K. / Skrzypczak-Jankun, E. / McCabe, N.P. / Selman, S.H. / Jankun, J. | ||||||
Citation | Journal: INT.J.MOL.MED. / Year: 2003 Title: Structure of curcumin in complex with lipoxygenase and its significance in cancer. Authors: Skrzypczak-Jankun, E. / Zhou, K. / McCabe, N.P. / Selman, S.H. / Jankun, J. #1: Journal: Int.J.Mol.Med. / Year: 2000 Title: Curcumin Inhibits Lipooxygenase by Binding to its Center Cavity: Theoretical and X-Ray Evidence Authors: Skrzypczak-Jankun, E. / McCabe, N.P. / Selman, S.H. / Jankun, J. #2: Journal: Proteins / Year: 1997 Title: Structure of Soybean Lipoxygenase L3 and a Comparison with its L1 Isoenzyme Authors: Skrzypczak-Jankun, E. / Amzel, L.M. / Kroa, B.A. / Funk Jr., M.O. #3: Journal: Biochemistry / Year: 1998 Title: Structural and Thermochemical Characterization of Lipoxygenase-Catechol Complexes Authors: Pham, C. / Jankun, J. / Skrzypczak-Jankun, E. / Flowers II, R.A. / Funk Jr., M.O. #4: Journal: Biochemistry / Year: 1994 Title: Position 713 is Critical for Catalysis But not Iron Binding in Soybean Lipoxygenase 3 Authors: Kramer, J.A. / Johnson, K.R. / Dunham, W.R. / Sands, R.H. / Funk Jr., M.O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hu9.cif.gz | 190.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hu9.ent.gz | 149.3 KB | Display | PDB format |
PDBx/mmJSON format | 1hu9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hu/1hu9 ftp://data.pdbj.org/pub/pdb/validation_reports/hu/1hu9 | HTTPS FTP |
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-Related structure data
Related structure data | 1lnhS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 96919.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: COMPLEX WITH 4-HYDROPEROXY-2-METHOXY-PHENOL A PHOTODEGREDATION PRODUCT OF CURCUMIN Source: (natural) Glycine max (soybean) / Strain: BEESON-80 CULTIVAR / References: UniProt: P09186, linoleate 13S-lipoxygenase |
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#2: Chemical | ChemComp-FE / |
#3: Chemical | ChemComp-4HM / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop / pH: 5.3 Details: PEG 8000, phosphate-citrate buffer, sodium azide, pH 5.3, VAPOR DIFFUSION, SITTING DROP, temperature 296K |
-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 1, 1999 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→40 Å / Num. all: 45106 / Num. obs: 45106 / % possible obs: 95.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 3 % / Biso Wilson estimate: 29.5 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 2 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 1 / Num. unique all: 4304 / % possible all: 90.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1LNH Resolution: 2.2→40 Å / Rfactor Rfree error: 0.02 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.01 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber Details: DISORDERED REGIONS 1-8 WERE OMITTED FROM CALCULATIONS. DISORDERED REGIONS 33-45 WERE INCLUDED IN THE REFINEMENT, HOWEVER, THE HIGH B-FACTOR INDICATE DISORDER AND LOW RELIABILITY FOR THIS ...Details: DISORDERED REGIONS 1-8 WERE OMITTED FROM CALCULATIONS. DISORDERED REGIONS 33-45 WERE INCLUDED IN THE REFINEMENT, HOWEVER, THE HIGH B-FACTOR INDICATE DISORDER AND LOW RELIABILITY FOR THIS LOOP. THE IRON BINDING SITE CONSISTS OF HIS 518, HIS 523, HIS 709 ASN 713, ILE 857 (C-TERMINAL) AND 4HM 861.THESE LIGANDS ARE ALL COVALENTLY BOUND TO IRON FE 858 IN AN OCTAHEDRAL COORDINATION.
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Displacement parameters | Biso mean: 35.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.24 Å / Luzzati d res low obs: 5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→40 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12
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Xplor file |
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