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- PDB-4bpm: Crystal structure of a human integral membrane enzyme -

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Basic information

Entry
Database: PDB / ID: 4bpm
TitleCrystal structure of a human integral membrane enzyme
ComponentsPROSTAGLANDIN E SYNTHASE, FUSION PEPTIDE
KeywordsISOMERASE / 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
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 / Prostaglandin E synthase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.08 Å
AuthorsLi, D. / Wang, M. / Olieric, V. / Caffrey, M.
CitationJournal: 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
DepositionMay 27, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1May 14, 2014Group: Database references
Revision 1.2Mar 15, 2017Group: Source and taxonomy
Revision 1.3Mar 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.4Apr 3, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROSTAGLANDIN E SYNTHASE, FUSION PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2873
Polymers20,3611
Non-polymers9262
Water66737
1
A: PROSTAGLANDIN E SYNTHASE, FUSION PEPTIDE
hetero molecules

A: PROSTAGLANDIN E SYNTHASE, FUSION PEPTIDE
hetero molecules

A: PROSTAGLANDIN E SYNTHASE, FUSION PEPTIDE
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 operation3_555-x+y,-x,z1
crystal symmetry operation2_555-y,x-y,z1
Buried area11820 Å2
ΔGint-53.7 kcal/mol
Surface area23540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.400, 86.400, 181.120
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein PROSTAGLANDIN E SYNTHASE, FUSION PEPTIDE / / 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 / PROSTAGLANDIN E2 SYNTHASE 1


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
#2: Chemical ChemComp-GSH / GLUTATHIONE / 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 / Water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE 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. A FUSION PEPTIDE LPAALRAALLGRLRTLRPWADYKDDDDK WAS ADDED IN THE C-TERMINUS.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.21 Å3/Da / Density % sol: 61.65 % / Description: NONE
Crystal growTemperature: 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.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.003319
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 2, 2012 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.003319 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 2.08→2.13 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 2.5 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
SHELXphasing
RefinementMethod 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
RfactorNum. reflection% reflection
Rfree0.2182 794 5 %
Rwork0.1999 --
obs0.2009 15904 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.27 Å2
Refinement stepCycle: LAST / Resolution: 2.08→36.639 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1292 0 61 37 1390
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031427
X-RAY DIFFRACTIONf_angle_d0.7631956
X-RAY DIFFRACTIONf_dihedral_angle_d11.19542
X-RAY DIFFRACTIONf_chiral_restr0.043217
X-RAY DIFFRACTIONf_plane_restr0.004268
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.08-2.21030.27371340.24912476X-RAY DIFFRACTION100
2.2103-2.38090.2541380.22442483X-RAY DIFFRACTION100
2.3809-2.62050.24741300.2112506X-RAY DIFFRACTION100
2.6205-2.99950.19691310.18732499X-RAY DIFFRACTION100
2.9995-3.77850.21161320.18552525X-RAY DIFFRACTION100
3.7785-36.64450.2081290.19922621X-RAY DIFFRACTION99

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