[English] 日本語
Yorodumi- PDB-1fe2: CRYSTAL STRUCTURE OF DIHOMO-GAMMA-LINOLEIC ACID BOUND IN THE CYCL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fe2 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF DIHOMO-GAMMA-LINOLEIC ACID BOUND IN THE CYCLOOXYGENASE CHANNEL OF PROSTAGLANDIN ENDOPEROXIDE H SYNTHASE-1. | |||||||||
Components | PROSTAGLANDIN ENDOPEROXIDE H SYNTHASE-1 | |||||||||
Keywords | OXIDOREDUCTASE / Membrane Protein / Fatty Acid / Dihomo-Gamma-Linoleic Acid / Peroxidase / Dioxygenase | |||||||||
Function / homology | Function and homology information prostaglandin-endoperoxide synthase / prostaglandin-endoperoxide synthase activity / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / cyclooxygenase pathway / prostaglandin biosynthetic process / regulation of blood pressure / peroxidase activity / response to oxidative stress / neuron projection / intracellular membrane-bounded organelle ...prostaglandin-endoperoxide synthase / prostaglandin-endoperoxide synthase activity / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / cyclooxygenase pathway / prostaglandin biosynthetic process / regulation of blood pressure / peroxidase activity / 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 / Resolution: 3 Å | |||||||||
Authors | Thuresson, E.D. / Malkowski, M.G. / Lakkides, K.M. / Smith, W.L. / Garavito, R.M. | |||||||||
Citation | 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. #1: Journal: To be published Title: Structure of Prostaglandin Synthase Complexed with Arachidonic Acid. Authors: Malkowski, M.G. / Ginell, S.L. / Smith, W.L. / Garavito, R.M. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1fe2.cif.gz | 118.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1fe2.ent.gz | 95.6 KB | Display | PDB format |
PDBx/mmJSON format | 1fe2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1fe2_validation.pdf.gz | 798.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1fe2_full_validation.pdf.gz | 808.2 KB | Display | |
Data in XML | 1fe2_validation.xml.gz | 19.8 KB | Display | |
Data in CIF | 1fe2_validation.cif.gz | 28.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fe/1fe2 ftp://data.pdbj.org/pub/pdb/validation_reports/fe/1fe2 | HTTPS FTP |
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 66164.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ISOLATED FROM SEMINAL VESSICLES / Source: (natural) Ovis aries (sheep) References: GenBank: AAA31511, UniProt: P05979*PLUS, prostaglandin-endoperoxide synthase |
---|
-Sugars , 3 types, 6 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...beta-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: Sugar | |
---|
-Non-polymers , 3 types, 62 molecules
#5: Chemical | ChemComp-COH / |
---|---|
#6: Chemical | ChemComp-LAX / |
#7: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
---|
-Sample preparation
Crystal | Density Matthews: 3.73 Å3/Da / Density % sol: 67.07 % | ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.03321 |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Mar 7, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03321 Å / Relative weight: 1 |
Reflection | Resolution: 3→20 Å / Num. all: 20660 / Num. obs: 20099 / % possible obs: 97.4 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.122 / Net I/σ(I): 27.2 |
Reflection shell | Resolution: 3→3.1 Å / Rmerge(I) obs: 0.589 / % possible all: 92.8 |
Reflection | *PLUS % possible obs: 94 % |
Reflection shell | *PLUS % possible obs: 83 % |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 3→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber Details: Used MLF target in CNS utilizing bulk solvent and overall B-factor corrections
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→20 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 18526 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
|