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- PDB-8pyv: Structure of Human PS-1 GSH-analog complex, solved at wavelength ... -

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Basic information

Entry
Database: PDB / ID: 8pyv
TitleStructure of Human PS-1 GSH-analog complex, solved at wavelength 2.755 A
ComponentsProstaglandin E synthase
KeywordsIMMUNE SYSTEM / membrane protein
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 (MAPEG) protein / Membrane associated eicosanoid/glutathione metabolism-like domain superfamily / MAPEG family
Similarity search - Domain/homology
Chem-48T / PALMITIC ACID / Prostaglandin E synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.77 Å
AuthorsDuman, R. / El Omari, K. / Mykhaylyk, V. / Orr, C. / Wagner, A. / Vogeley, L. / Brown, D.G.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Diamond Light Source United Kingdom
CitationJournal: Commun Chem / Year: 2023
Title: Experimental phasing opportunities for macromolecular crystallography at very long wavelengths.
Authors: El Omari, K. / Duman, R. / Mykhaylyk, V. / Orr, C.M. / Latimer-Smith, M. / Winter, G. / Grama, V. / Qu, F. / Bountra, K. / Kwong, H.S. / Romano, M. / Reis, R.I. / Vogeley, L. / Vecchia, L. / ...Authors: El Omari, K. / Duman, R. / Mykhaylyk, V. / Orr, C.M. / Latimer-Smith, M. / Winter, G. / Grama, V. / Qu, F. / Bountra, K. / Kwong, H.S. / Romano, M. / Reis, R.I. / Vogeley, L. / Vecchia, L. / Owen, C.D. / Wittmann, S. / Renner, M. / Senda, M. / Matsugaki, N. / Kawano, Y. / Bowden, T.A. / Moraes, I. / Grimes, J.M. / Mancini, E.J. / Walsh, M.A. / Guzzo, C.R. / Owens, R.J. / Jones, E.Y. / Brown, D.G. / Stuart, D.I. / Beis, K. / Wagner, A.
History
DepositionJul 26, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Prostaglandin E synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1384
Polymers17,1231
Non-polymers1,0143
Water59433
1
A: Prostaglandin E synthase
hetero molecules

A: Prostaglandin E synthase
hetero molecules

A: Prostaglandin E synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,41312
Polymers51,3703
Non-polymers3,0439
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area10010 Å2
ΔGint-37 kcal/mol
Surface area17830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.200, 77.200, 122.060
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3
Components on special symmetry positions
IDModelComponents
11A-324-

HOH

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Components

#1: Protein Prostaglandin E synthase / / Glutathione peroxidase PTGES / Glutathione transferase PTGES / Microsomal glutathione S-transferase ...Glutathione peroxidase PTGES / Glutathione transferase PTGES / Microsomal glutathione S-transferase 1-like 1 / MGST1-L1 / Microsomal prostaglandin E synthase 1 / MPGES-1 / p53-induced gene 12 protein


Mass: 17123.322 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 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: O14684, prostaglandin-E synthase, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases, glutathione transferase
#2: Chemical ChemComp-PLM / PALMITIC ACID / Palmitic acid


Mass: 256.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H32O2
#3: Chemical ChemComp-48T / L-gamma-glutamyl-S-(2-biphenyl-4-yl-2-oxoethyl)-L-cysteinylglycine


Mass: 501.552 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H27N3O7S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 4.09 Å3/Da / Density % sol: 69.91 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 100 mM Tris pH 8 , % PEG400, 100 mM NaCl and 1mM TCEP

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I23 / Wavelength: 2.7552 Å
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Aug 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.7552 Å / Relative weight: 1
ReflectionResolution: 1.77→58.64 Å / Num. obs: 26090 / % possible obs: 97.51 % / Redundancy: 17.5 % / CC1/2: 0.999 / Net I/σ(I): 21.23
Reflection shellResolution: 1.772→1.836 Å / Num. unique obs: 2383 / CC1/2: 0.21

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.77→58.64 Å / Cross valid method: FREE R-VALUE / σ(F): 2.58 / Phase error: 31.1107
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2138 1276 4.96 %
Rwork0.1979 24460 -
obs0.2127 25736 97.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.04 Å2
Refinement stepCycle: LAST / Resolution: 1.77→58.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1159 0 43 33 1235
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01111244
X-RAY DIFFRACTIONf_angle_d1.13881682
X-RAY DIFFRACTIONf_chiral_restr0.0528187
X-RAY DIFFRACTIONf_plane_restr0.0128210
X-RAY DIFFRACTIONf_dihedral_angle_d16.8992185
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.840.53041170.6342181X-RAY DIFFRACTION74.08
1.84-1.930.61241390.50932767X-RAY DIFFRACTION94.73
1.93-2.030.36281470.3522801X-RAY DIFFRACTION95.01
2.03-2.150.2611490.26592796X-RAY DIFFRACTION94.94
2.15-2.320.23231180.23412796X-RAY DIFFRACTION95.95
2.32-2.550.22611600.21472764X-RAY DIFFRACTION94.53
2.56-2.920.1951640.19612767X-RAY DIFFRACTION94.4
2.93-3.680.22461190.18082817X-RAY DIFFRACTION95.95
3.69-58.640.17831430.17392791X-RAY DIFFRACTION95.13
Refinement TLS params.Method: refined / Origin x: 10.0136608101 Å / Origin y: -1.2560639099 Å / Origin z: 49.5994006691 Å
111213212223313233
T0.258189905617 Å20.00381014982209 Å20.000561346834184 Å2-0.257883279113 Å20.00238555277852 Å2--0.228930182538 Å2
L0.267485835479 °2-0.0404106021578 °20.0149831945032 °2-0.352724889462 °2-0.116701283372 °2--0.35897744621 °2
S0.0268236392853 Å °-0.0122344397997 Å °0.00217232236102 Å °-0.00713445036283 Å °-0.0268075162224 Å °-0.0475210042332 Å °0.030095614904 Å °0.0878669762196 Å °-0.00287680827229 Å °
Refinement TLS groupSelection details: all

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