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Yorodumi- PDB-1diy: CRYSTAL STRUCTURE OF ARACHIDONIC ACID BOUND IN THE CYCLOOXYGENASE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1diy | |||||||||
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Title | CRYSTAL STRUCTURE OF ARACHIDONIC ACID BOUND IN THE CYCLOOXYGENASE ACTIVE SITE OF PGHS-1 | |||||||||
Components | PROSTAGLANDIN H2 SYNTHASE-1Cyclooxygenase | |||||||||
Keywords | OXIDOREDUCTASE / ARACHIDONIC ACID / MEMBRANE PROTEIN / PEROXIDASE / DIOXYGENASE | |||||||||
Function / homology | Function and homology information prostaglandin-endoperoxide synthase / prostaglandin-endoperoxide synthase activity / cyclooxygenase pathway / prostaglandin biosynthetic process / dioxygenase activity / peroxidase activity / regulation of blood pressure / response to oxidative stress / intracellular membrane-bounded organelle / heme binding ...prostaglandin-endoperoxide synthase / prostaglandin-endoperoxide synthase activity / cyclooxygenase pathway / prostaglandin biosynthetic process / dioxygenase activity / peroxidase activity / regulation of blood pressure / response to oxidative stress / 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 Å | |||||||||
Authors | Malkowski, M.G. / Ginell, S.L. / Smith, W.L. / Garavito, R.M. | |||||||||
Citation | 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 | 1diy.cif.gz | 128.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1diy.ent.gz | 97 KB | Display | PDB format |
PDBx/mmJSON format | 1diy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/di/1diy ftp://data.pdbj.org/pub/pdb/validation_reports/di/1diy | HTTPS FTP |
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-Related structure data
Related structure data | 1prhS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 63724.141 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 , 4 types, 7 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 | ChemComp-BOG / |
-Non-polymers , 3 types, 111 molecules
#6: Chemical | ChemComp-COH / |
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#7: Chemical | ChemComp-ACD / |
#8: 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: 4.1 Å3/Da / Density % sol: 69 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: LITHIUM CHLORIDE, SODIUM AZIDE, SODIUM CITRATE, 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: 1.03321 |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Aug 21, 1999 |
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→9 Å / Num. all: 630793 / Num. obs: 19163 / % possible obs: 93.8 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.067 |
Reflection shell | Resolution: 3→3.1 Å / Rmerge(I) obs: 0.347 / % possible all: 81.4 |
Reflection | *PLUS % possible obs: 93 % |
Reflection shell | *PLUS % possible obs: 81 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1PRH MOLECULE B, PROTEIN ONLY Resolution: 3→9 Å / σ(F): 2 / Stereochemistry target values: ENGH & HUBER Details: USED THE MLF TARGET IN CNS UTILIZING BULK SOLVENT AND OVERALL B-FACTOR CORRECTIONS
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.1 Å / Total num. of bins used: 10
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Xplor file | Serial no: 1 / Param file: protein_rep.param / Topol file: protein.top | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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