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- PDB-4al1: Crystal structure of Human PS-1 GSH-analog complex -

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Basic information

Entry
Database: PDB / ID: 4al1
TitleCrystal structure of Human PS-1 GSH-analog complex
ComponentsPROSTAGLANDIN E SYNTHASE
KeywordsISOMERASE / MEMBRANE PROTEIN / LIPID BIOSYNTHESIS
Function / homology
Function and homology information


prostaglandin-E synthase / prostaglandin-E synthase activity / regulation of fever generation / prostaglandin-D synthase activity / glutathione binding / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / positive regulation of prostaglandin secretion / 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 / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / positive regulation of prostaglandin secretion / 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
Chem-48T / PALMITIC ACID / Prostaglandin E synthase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsSjogren, T. / Nord, J. / Ek, M. / Johansson, P. / Liu, G. / Geschwindner, S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Crystal Structure of Microsomal Prostaglandin E2 Synthase Provides Insight Into Diversity in the Mapeg Superfamily.
Authors: Sjogren, T. / Nord, J. / Ek, M. / Johansson, P. / Liu, G. / Geschwindner, S.
History
DepositionFeb 29, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 6, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2013Group: Database references
Revision 1.2Apr 3, 2013Group: Database references
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5266
Polymers17,1231
Non-polymers1,4035
Water1,44180
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)55,57818
Polymers51,3703
Non-polymers4,20815
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 area13240 Å2
ΔGint-51.6 kcal/mol
Surface area16500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.623, 76.623, 123.349
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-2054-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein PROSTAGLANDIN E 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: 17123.322 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: O14684, prostaglandin-E synthase
#2: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 84 molecules

#3: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H32O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O

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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: 4.1 Å3/Da / Density % sol: 69.99 % / Description: NONE
Crystal growpH: 8 / Details: pH 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.9795
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 15, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. obs: 19681 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 3 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 5.1
Reflection shellResolution: 1.95→2 Å / Redundancy: 3 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 1.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AL0

4al0


Resolution: 1.95→30 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.891 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.17225 973 5.1 %RANDOM
Rwork0.172 ---
obs0.163 18156 97.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.803 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20.08 Å20 Å2
2--0.17 Å20 Å2
3----0.25 Å2
Refinement stepCycle: LAST / Resolution: 1.95→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1138 0 82 80 1300
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2075142
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.6120.76952
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.12215205
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7231513
X-RAY DIFFRACTIONr_chiral_restr0.0740.2197
X-RAY DIFFRACTIONr_gen_planes_refined
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 68 -
Rwork0.193 1235 -
obs--91.06 %

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