+Open data
-Basic information
Entry | Database: PDB / ID: 3n8v | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal Structure of Unoccupied Cyclooxygenase-1 | |||||||||
Components | Prostaglandin G/H synthase 1 | |||||||||
Keywords | OXIDOREDUCTASE / cox-1 / cyclooxygenase / peroxidase / prostaglandin / heme / unoccupied / 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: 3.05 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3n8v.cif.gz | 475.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3n8v.ent.gz | 392.5 KB | Display | PDB format |
PDBx/mmJSON format | 3n8v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3n8v_validation.pdf.gz | 3.8 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3n8v_full_validation.pdf.gz | 3.8 MB | Display | |
Data in XML | 3n8v_validation.xml.gz | 43.9 KB | Display | |
Data in CIF | 3n8v_validation.cif.gz | 60.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n8/3n8v ftp://data.pdbj.org/pub/pdb/validation_reports/n8/3n8v | HTTPS FTP |
-Related structure data
Related structure data | 3n8wC 3n8xC 3n8yC 3n8zC 1q4gS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
|
-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 |
---|
-Sugars , 5 types, 11 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #5: Polysaccharide | beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1- ...beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #7: Sugar | ChemComp-BOG / |
---|
-Non-polymers , 3 types, 227 molecules
#6: Chemical | #8: Chemical | ChemComp-GOL / | #9: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.84 Å3/Da / Density % sol: 68 % |
---|---|
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 | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 | |||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 22, 2009 | |||||||||||||||
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
| |||||||||||||||
Reflection | Resolution: 3.05→40.2 Å / Num. obs: 36921 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 11 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 24 | |||||||||||||||
Reflection shell | Resolution: 3.05→3.13 Å / % possible all: 97.5 |
-Processing
Software | Name: REFMAC / Version: 5.5.0102 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1Q4G Resolution: 3.05→40.2 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.905 / SU B: 29.759 / SU ML: 0.23 / Cross valid method: THROUGHOUT / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 68.31 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.05→40.2 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.05→3.13 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|