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Yorodumi- PDB-1igx: Crystal Structure of Eicosapentanoic Acid Bound in the Cyclooxyge... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1igx | |||||||||
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Title | Crystal Structure of Eicosapentanoic Acid Bound in the Cyclooxygenase Channel of Prostaglandin Endoperoxide H Synthase-1. | |||||||||
Components | Prostaglandin Endoperoxide H Synthase-1 | |||||||||
Keywords | OXIDOREDUCTASE / membrane protein / fatty acid / eicosapentanoic acid / peroxidase / dioxygenase | |||||||||
Function / homology | Function and homology information prostaglandin-endoperoxide synthase / prostaglandin-endoperoxide synthase activity / cyclooxygenase pathway / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / prostaglandin biosynthetic process / peroxidase activity / regulation of blood pressure / response to oxidative stress / neuron projection / intracellular membrane-bounded organelle ...prostaglandin-endoperoxide synthase / prostaglandin-endoperoxide synthase activity / cyclooxygenase pathway / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / prostaglandin biosynthetic process / peroxidase activity / regulation of blood pressure / response to oxidative stress / neuron projection / intracellular membrane-bounded organelle / heme binding / endoplasmic reticulum membrane / protein homodimerization activity / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Ovis aries (sheep) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | |||||||||
Authors | Malkowski, M.G. / Thuresson, E.D. / Smith, W.L. / Garavito, R.M. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2001 Title: Structure of eicosapentaenoic and linoleic acids in the cyclooxygenase site of prostaglandin endoperoxide H synthase-1. Authors: Malkowski, M.G. / Thuresson, E.D. / Lakkides, K.M. / Rieke, C.J. / Micielli, R. / Smith, W.L. / Garavito, R.M. #1: Journal: J.Biol.Chem. / Year: 2001 Title: Mutational and X-ray Crystallographic analysis of the Interaction of Dihomo-Gamma-Linolenic Acid with Prostaglandin Endoperoxide H Synthases. Authors: Thuresson, E.D. / Malkowski, M.G. / Lakkides, K.M. / Rieke, C.J. / Mulichak, A.M. / Ginell, S.L. / Garavito, R.M. / Smith, W.L. #2: Journal: Science / Year: 2000 Title: The Productive Conformation of Arachidonic Acid Bound to Prostaglandin Synthase. Authors: Malkowski, M.G. / Ginell, S.L. / Smith, W.L. / Garavito, R.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1igx.cif.gz | 127.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1igx.ent.gz | 95.3 KB | Display | PDB format |
PDBx/mmJSON format | 1igx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1igx_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
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Full document | 1igx_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 1igx_validation.xml.gz | 28.9 KB | Display | |
Data in CIF | 1igx_validation.cif.gz | 39.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ig/1igx ftp://data.pdbj.org/pub/pdb/validation_reports/ig/1igx | HTTPS FTP |
-Related structure data
Related structure data | 1igzC 1diyS 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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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 66164.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: seminal vessicle References: GenBank: 165844, UniProt: P05979*PLUS, prostaglandin-endoperoxide synthase |
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-Sugars , 5 types, 6 molecules
#2: Polysaccharide | 2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||
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#3: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||
#4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||
#5: Sugar | #6: Sugar | ChemComp-BGC / | |
-Non-polymers , 3 types, 58 molecules
#7: Chemical | ChemComp-COH / |
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#8: Chemical | ChemComp-EPA / |
#9: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.73 Å3/Da / Density % sol: 67.02 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: lithium chloride, sodium azide, citric acid, n-octyl-glucoside, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0332 Å |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Aug 20, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→20 Å / Num. all: 18711 / Num. obs: 18578 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.086 / Net I/σ(I): 25.9 |
Reflection shell | Resolution: 3.1→3.21 Å / Rmerge(I) obs: 0.464 / Mean I/σ(I) obs: 4.2 / % possible all: 99.6 |
Reflection | *PLUS Num. all: 18711 / Num. obs: 17814 / % possible obs: 92 % |
Reflection shell | *PLUS % possible obs: 78 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1DIY Resolution: 3.1→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.1→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.1→3.21 Å
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 3.1 Å / Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 4 % / Rfactor obs: 0.23 / Rfactor Rfree: 0.296 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 3.1 Å / Rfactor Rfree: 0.345 / Rfactor Rwork: 0.306 |