+Open data
-Basic information
Entry | Database: PDB / ID: 4al0 | ||||||
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Title | Crystal structure of Human PS-1 | ||||||
Components | PROSTAGLANDIN E SYNTHASE | ||||||
Keywords | ISOMERASE / MEMBRANE PROTEIN / LIPID BIOSYNTHESIS | ||||||
Function / homology | Function and homology information regulation of fever generation / prostaglandin-E synthase / prostaglandin-E synthase activity / prostaglandin-D synthase activity / positive regulation of prostaglandin secretion / glutathione binding / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / glutathione peroxidase activity / prostaglandin biosynthetic process / prostaglandin metabolic process ...regulation of fever generation / prostaglandin-E synthase / prostaglandin-E synthase activity / prostaglandin-D synthase activity / positive regulation of prostaglandin secretion / glutathione binding / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / glutathione peroxidase activity / prostaglandin biosynthetic process / prostaglandin metabolic process / nuclear envelope lumen / glutathione transferase / glutathione transferase activity / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / sensory perception of pain / regulation of inflammatory response / cell population proliferation / negative regulation of cell population proliferation / endoplasmic reticulum membrane / perinuclear region of cytoplasm / signal transduction / membrane Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.16 Å | ||||||
Authors | Sjogren, T. / Nord, J. / Ek, M. / Johansson, P. / Liu, G. / Geschwindner, S. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2013 Title: Crystal Structure of Microsomal Prostaglandin E2 Synthase Provides Insight Into Diversity in the Mapeg Superfamily. Authors: Sjogren, T. / Nord, J. / Ek, M. / Johansson, P. / Liu, G. / Geschwindner, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4al0.cif.gz | 83.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4al0.ent.gz | 62.7 KB | Display | PDB format |
PDBx/mmJSON format | 4al0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/al/4al0 ftp://data.pdbj.org/pub/pdb/validation_reports/al/4al0 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 17123.322 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: O14684, prostaglandin-E synthase | ||||
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#2: Chemical | ChemComp-GSH / | ||||
#3: Chemical | #4: Sugar | #5: 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: 69.99 % / Description: NONE |
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Crystal grow | pH: 8 / Details: pH 8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.98 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 9, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.16→58.53 Å / Num. obs: 89826 / % possible obs: 96.9 % / Observed criterion σ(I): 1 / Redundancy: 3.1 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 1.16→1.23 Å / Redundancy: 3 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 1.9 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 1.16→58.53 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.978 / SU B: 0.573 / SU ML: 0.012 / Cross valid method: THROUGHOUT / ESU R: 0.021 / ESU R Free: 0.02 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.U VALUES REFINED INDIVIDUALLY.
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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: 15.297 Å2
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Refinement step | Cycle: LAST / Resolution: 1.16→58.53 Å
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Refine LS restraints |
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