+Open data
-Basic information
Entry | Database: PDB / ID: 4bpm | ||||||
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Title | Crystal structure of a human integral membrane enzyme | ||||||
Components | PROSTAGLANDIN E SYNTHASE, FUSION PEPTIDE | ||||||
Keywords | ISOMERASE / CANCER / DRUG TARGET / IN MESO CRYSTALLIZATION / INFLAMMATION / INHIBITOR / LEUKOTRIENE C4 SYNTHASE / LIPID METABOLISM / MEMBRANE-ASSOCIATED PROTEINS IN EICOSANOID AND GLUTATHIONE METABOLISM / MAPAG / MEMBRANE PROTEIN / MPGES1 / PAIN / MICROCRYSTAL / ANOMALOUS DISPERSION / SULFUR-SAD / S-SAD | ||||||
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) SYNTHETIC CONSTRUCT (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.08 Å | ||||||
Authors | Li, D. / Wang, M. / Olieric, V. / Caffrey, M. | ||||||
Citation | Journal: Cryst.Growth Des. / Year: 2014 Title: Crystallizing Membrane Proteins in the Lipidic Mesophase. Experience with Human Prostaglandin E2 Synthase 1 and an Evolving Strategy. Authors: Li, D. / Howe, N. / Dukkipati, A. / Shah, S.T.A. / Bax, B.D. / Edge, C. / Bridges, A. / Hardwicke, P. / Singh, O.M.P. / Giblin, G. / Pautsch, A. / Pfau, R. / Schnapp, G. / Wang, M. / Olieric, V. / Caffrey, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bpm.cif.gz | 49.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bpm.ent.gz | 35.1 KB | Display | PDB format |
PDBx/mmJSON format | 4bpm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bp/4bpm ftp://data.pdbj.org/pub/pdb/validation_reports/bp/4bpm | HTTPS FTP |
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-Related structure data
Related structure data | |
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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
#1: Protein | Mass: 20360.932 Da / Num. of mol.: 1 / Fragment: GSH-BINDING MOTIF, RESIDUES 10-152 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human), (gene. exp.) SYNTHETIC CONSTRUCT (others) Plasmid: PFB1-6H-MPGES (10-152)-F-LTC4S / 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 | ChemComp-LVJ / |
#4: Water | ChemComp-HOH / |
Sequence details | THE N-TERMINAL 9 AMINO ACIDS MPAHSLVMS WERE OMITTED. A 6- HIS TAG WAS PLACED AT THE N-TERMINUS. A ...THE N-TERMINAL 9 AMINO ACIDS MPAHSLVMS WERE OMITTED. A 6- HIS TAG WAS PLACED AT THE N-TERMINUS. A POINT MUTATION L152F WAS INTRODUCED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.21 Å3/Da / Density % sol: 61.65 % / Description: NONE |
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Crystal grow | Temperature: 277 K / Method: lipidic cubic phase / pH: 6.7 Details: 8 %(V/V) 2-METHYL-2,4, -PENTANEDIOL (MPD), 0.4 M POTASSIUM NITRATE, 0.1 M POTASSIUM CITRATE, 0.1 M N-(CARBAMOYLMETHYL)IMINODIACETIC ACID (ADA) SODIUM PH 6.7. CRYSTALLIZED USING THE IN MESO ...Details: 8 %(V/V) 2-METHYL-2,4, -PENTANEDIOL (MPD), 0.4 M POTASSIUM NITRATE, 0.1 M POTASSIUM CITRATE, 0.1 M N-(CARBAMOYLMETHYL)IMINODIACETIC ACID (ADA) SODIUM PH 6.7. CRYSTALLIZED USING THE IN MESO (LIPIDIC CUBIC PHASE, LCP) METHOD AT 4 DEGREES CELCIUS WITH THE 8.8 MONOACYLGLYCEROL (8.8 MAG) DOPED WITH 2 MOL% OF DIOLEOYL PHOSPHATIDYLCHOLINE (DOPC) AS THE HOSTING LIPID. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.003319 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 2, 2012 / Details: MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.003319 Å / Relative weight: 1 |
Reflection | Resolution: 2.08→36.64 Å / Num. obs: 15904 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Biso Wilson estimate: 38.6 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 2.08→2.13 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 2.5 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 2.08→36.639 Å / SU ML: 0.11 / σ(F): 1.35 / Phase error: 22.21 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.27 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.08→36.639 Å
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Refine LS restraints |
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LS refinement shell |
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