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Yorodumi- PDB-3n8z: Crystal Structure of Cyclooxygenase-1 in Complex with Flurbiprofen -
+Open data
-Basic information
Entry | Database: PDB / ID: 3n8z | |||||||||
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Title | Crystal Structure of Cyclooxygenase-1 in Complex with Flurbiprofen | |||||||||
Components | Prostaglandin G/H synthase 1 | |||||||||
Keywords | OXIDOREDUCTASE / cox-1 / cyclooxygenase / peroxidase / prostaglandin / heme / flurbiprofen / merohedral twinned | |||||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | |||||||||
Authors | Sidhu, R.S. | |||||||||
Citation | Journal: Biochemistry / Year: 2010 Title: Comparison of Cyclooxygenase-1 Crystal Structures: Cross-Talk between Monomers Comprising Cyclooxygenase-1 Homodimers Authors: Sidhu, R.S. / Lee, J.Y. / Yuan, C. / Smith, W.L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3n8z.cif.gz | 472.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3n8z.ent.gz | 391.7 KB | Display | PDB format |
PDBx/mmJSON format | 3n8z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3n8z_validation.pdf.gz | 3.4 MB | Display | wwPDB validaton report |
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Full document | 3n8z_full_validation.pdf.gz | 3.4 MB | Display | |
Data in XML | 3n8z_validation.xml.gz | 43.5 KB | Display | |
Data in CIF | 3n8z_validation.cif.gz | 58.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n8/3n8z ftp://data.pdbj.org/pub/pdb/validation_reports/n8/3n8z | HTTPS FTP |
-Related structure data
Related structure data | 3n8vC 3n8wC 3n8xC 3n8yC 1q46S C: citing same article (ref.) 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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Noncrystallographic symmetry (NCS) | NCS domain:
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Details | biological unit is the same as asym. |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 63724.141 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ovis aries (sheep) / Strain: SHEEP / Gene: COX1, PTGS1 / Plasmid: PFASTBAC-HTOCOX-1 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF21 References: UniProt: P05979, prostaglandin-endoperoxide synthase |
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-Sugars , 4 types, 10 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 | Source method: isolated from a genetically manipulated source #4: Polysaccharide | alpha-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-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 #6: Sugar | ChemComp-BOG / |
-Non-polymers , 3 types, 139 molecules
#5: Chemical | #7: Chemical | #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: 3.87 Å3/Da / Density % sol: 68.19 % |
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Crystal grow | Temperature: 273 K / pH: 6.5 Details: SODIUM CITRATE, LITHIUM CHLORIDE, SODIUM AZIDE, N-OCTYL GLUCOSIDE, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 273K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1 | |||||||||||||||
Detector | Type: MAR225 / Detector: IMAGE PLATE / Date: Aug 19, 2006 | |||||||||||||||
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.9→31.63 Å / Num. obs: 43176 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 9.7 % / Rsym value: 0.105 / Net I/σ(I): 6.269 | |||||||||||||||
Reflection shell | Resolution: 2.9→2.97 Å / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1Q46 Resolution: 2.9→31.63 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.929 / SU B: 35.57 / SU ML: 0.272 / Cross valid method: THROUGHOUT / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 66.22 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→31.63 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 4383 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.9→2.97 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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