+Open data
-Basic information
Entry | Database: PDB / ID: 4wab | ||||||
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Title | Crystal structure of mPGES1 solved by native-SAD phasing | ||||||
Components | Prostaglandin E synthase,Leukotriene C4 synthase | ||||||
Keywords | ISOMERASE / native-SAD / 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 / membrane => GO:0016020 / 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: 2.704 Å | ||||||
Authors | Weinert, T. / Li, D. / Howe, N. / Caffrey, M. / Wang, M. | ||||||
Citation | Journal: Nat.Methods / Year: 2015 Title: Fast native-SAD phasing for routine macromolecular structure determination. Authors: Weinert, T. / Olieric, V. / Waltersperger, S. / Panepucci, E. / Chen, L. / Zhang, H. / Zhou, D. / Rose, J. / Ebihara, A. / Kuramitsu, S. / Li, D. / Howe, N. / Schnapp, G. / Pautsch, A. / ...Authors: Weinert, T. / Olieric, V. / Waltersperger, S. / Panepucci, E. / Chen, L. / Zhang, H. / Zhou, D. / Rose, J. / Ebihara, A. / Kuramitsu, S. / Li, D. / Howe, N. / Schnapp, G. / Pautsch, A. / Bargsten, K. / Prota, A.E. / Surana, P. / Kottur, J. / Nair, D.T. / Basilico, F. / Cecatiello, V. / Pasqualato, S. / Boland, A. / Weichenrieder, O. / Wang, B.C. / Steinmetz, M.O. / Caffrey, M. / Wang, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wab.cif.gz | 82.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wab.ent.gz | 61.9 KB | Display | PDB format |
PDBx/mmJSON format | 4wab.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4wab_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4wab_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4wab_validation.xml.gz | 8.3 KB | Display | |
Data in CIF | 4wab_validation.cif.gz | 10.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wa/4wab ftp://data.pdbj.org/pub/pdb/validation_reports/wa/4wab | HTTPS FTP |
-Related structure data
Related structure data | 4pgoC 4piiC 4r8tC 4r8uC 4tn8C 4tnoC 4wauC 4wbqC 4wbxC C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 20360.932 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PTGES, MGST1L1, MPGES1, PGES, PIG12, LTC4S / Plasmid: PFB1-6H-MPGES (10-152)-F-LTC4S / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: O14684, UniProt: B5MCC3, prostaglandin-E synthase |
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#2: Chemical | ChemComp-GSH / |
#3: Chemical | ChemComp-LVJ / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.21 Å3/Da / Density % sol: 61.62 % |
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Crystal grow | Temperature: 293 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: X06DA / Wavelength: 2.0664 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 2, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 2.0664 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 27480 / % possible obs: 99.4 % / Redundancy: 58.2 % / Net I/σ(I): 31.07 |
Reflection shell | Resolution: 2.7→2.77 Å / Mean I/σ(I) obs: 3.72 / Num. unique all: 1855 / % possible all: 92 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.704→43.36 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 22.06 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.704→43.36 Å
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Refine LS restraints |
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LS refinement shell |
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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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