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- PDB-4wab: Crystal structure of mPGES1 solved by native-SAD phasing -

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Basic information

Entry
Database: PDB / ID: 4wab
TitleCrystal structure of mPGES1 solved by native-SAD phasing
ComponentsProstaglandin E synthase,Leukotriene C4 synthase
KeywordsISOMERASE / 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


prostaglandin-E synthase / prostaglandin-E synthase activity / regulation of fever generation / prostaglandin-D synthase activity / glutathione binding / positive regulation of prostaglandin secretion / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / glutathione peroxidase activity / prostaglandin biosynthetic process / prostaglandin metabolic process ...prostaglandin-E synthase / prostaglandin-E synthase activity / regulation of fever generation / prostaglandin-D synthase activity / glutathione binding / positive regulation of prostaglandin secretion / 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
Microsomal glutathione S-transferase 1-like / : / Membrane associated eicosanoid/glutathione metabolism-like domain / Membrane-associated, eicosanoid/glutathione metabolism (MAPEG) protein / Membrane associated eicosanoid/glutathione metabolism-like domain superfamily / MAPEG family / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
GLUTATHIONE / Chem-LVJ / Leukotriene C4 synthase / Prostaglandin E synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.704 Å
AuthorsWeinert, T. / Li, D. / Howe, N. / Caffrey, M. / Wang, M.
CitationJournal: 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
DepositionAug 29, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 31, 2014Group: Database references
Revision 1.2Feb 11, 2015Group: Database references
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Prostaglandin E synthase,Leukotriene C4 synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2873
Polymers20,3611
Non-polymers9262
Water34219
1
A: Prostaglandin E synthase,Leukotriene C4 synthase
hetero molecules

A: Prostaglandin E synthase,Leukotriene C4 synthase
hetero molecules

A: Prostaglandin E synthase,Leukotriene C4 synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,8609
Polymers61,0833
Non-polymers2,7776
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area9920 Å2
ΔGint-69 kcal/mol
Surface area23570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.720, 86.720, 180.360
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-305-

HOH

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Components

#1: Protein Prostaglandin E synthase,Leukotriene C4 synthase / Microsomal glutathione S-transferase 1-like 1 / MGST1-L1 / Microsomal prostaglandin E synthase 1 / ...Microsomal glutathione S-transferase 1-like 1 / MGST1-L1 / Microsomal prostaglandin E synthase 1 / MPGES-1 / p53-induced gene 12 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
#2: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Chemical ChemComp-LVJ / 2-[[2,6-bis(chloranyl)-3-[(2,2-dimethylpropanoylamino)methyl]phenyl]amino]-1-methyl-6-(2-methyl-2-oxidanyl-propoxy)-N-[2,2,2-tris(fluoranyl)ethyl]benzimidazole-5-carboxamide


Mass: 618.475 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H32Cl2F3N5O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.21 Å3/Da / Density % sol: 61.62 %
Crystal growTemperature: 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.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 2.0664 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 2, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.0664 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 27480 / % possible obs: 99.4 % / Redundancy: 58.2 % / Net I/σ(I): 31.07
Reflection shellResolution: 2.7→2.77 Å / Mean I/σ(I) obs: 3.72 / Num. unique all: 1855 / % possible all: 92

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod 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
RfactorNum. reflection% reflection
Rfree0.2405 678 4.92 %
Rwork0.1777 --
obs0.1808 13774 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.704→43.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1278 0 61 19 1358
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091376
X-RAY DIFFRACTIONf_angle_d1.1021878
X-RAY DIFFRACTIONf_dihedral_angle_d13.164524
X-RAY DIFFRACTIONf_chiral_restr0.039208
X-RAY DIFFRACTIONf_plane_restr0.005259
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7044-2.91310.26011430.20772539X-RAY DIFFRACTION98
2.9131-3.20620.24141460.17442637X-RAY DIFFRACTION100
3.2062-3.670.21961350.16382616X-RAY DIFFRACTION100
3.67-4.62290.2481160.18112664X-RAY DIFFRACTION100
4.6229-43.36560.2391380.17622640X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.80980.7261-2.89931.1527-0.34889.2591-0.08780.0820.022-0.12370.1978-0.05210.2254-0.2843-0.23680.38420.0193-0.01980.42460.00060.50243.172637.024967.8429
21.0017-0.6077-0.00551.0446-0.39914.11940.0854-0.268-0.14350.17370.12430.1546-0.01650.0196-0.23390.48840.0011-0.01890.47750.00430.4454-0.273142.065478.481
31.2240.9527-0.84963.5574-1.17755.62050.16980.0530.24190.07280.0291-0.1470.18830.4142-0.38950.32450.05370.02340.3972-0.00590.536115.74740.863966.3778
42.2379-1.00350.86833.9456-2.09772.5859-0.04010.1041-0.0636-0.17160.27790.2573-0.18770.0417-0.2820.3581-0.08360.03290.5538-0.01510.391615.892953.393461.8892
57.3227-6.1683-5.81855.52365.33638.2596-0.73810.9445-1.01211.388-0.08970.27020.7736-0.42870.85340.5718-0.18490.04360.57550.15060.467918.520868.560842.7954
63.456-1.71592.15852.69932.20997.08140.02491.0259-0.2555-1.777-0.32751.2728-0.999-0.97960.29070.58310.0616-0.12310.78560.14260.637721.664974.863530.6111
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 40 )
2X-RAY DIFFRACTION2chain 'A' and (resid 41 through 91 )
3X-RAY DIFFRACTION3chain 'A' and (resid 92 through 124 )
4X-RAY DIFFRACTION4chain 'A' and (resid 125 through 152 )
5X-RAY DIFFRACTION5chain 'A' and (resid 153 through 162 )
6X-RAY DIFFRACTION6chain 'A' and (resid 163 through 170 )

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