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- PDB-1z9h: Microsomal prostaglandin E synthase type-2 -

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Basic information

Entry
Database: PDB / ID: 1z9h
TitleMicrosomal prostaglandin E synthase type-2
Componentsmembrane-associated prostaglandin E synthase-2
KeywordsISOMERASE / Membran associated protein / Prostaglandin E synthase / Indomethacin
Function / homology
Function and homology information


12-hydroxyheptadecatrienoic acid synthase activity / prostaglandin-E synthase / prostaglandin-E synthase activity / glutathione binding / prostaglandin biosynthetic process / lyase activity / Golgi membrane / heme binding / perinuclear region of cytoplasm / mitochondrion / identical protein binding
Similarity search - Function
Defensin A-like - #30 / Prostaglandin E synthase 2 / Prostaglandin E synthase 2, C-terminal / Defensin A-like / Glutaredoxin active site. / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutaredoxin domain profile. / Other non-globular / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 ...Defensin A-like - #30 / Prostaglandin E synthase 2 / Prostaglandin E synthase 2, C-terminal / Defensin A-like / Glutaredoxin active site. / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutaredoxin domain profile. / Other non-globular / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Special / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / INDOMETHACIN / Prostaglandin E synthase 2
Similarity search - Component
Biological speciesMacaca fascicularis (crab-eating macaque)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsYamada, T. / Komoto, J. / Watanabe, K. / Ohmiya, Y. / Takusagawa, F.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Crystal Structure and Possible Catalytic Mechanism of Microsomal Prostaglandin E Synthase Type 2 (mPGES-2).
Authors: Yamada, T. / Komoto, J. / Watanabe, K. / Ohmiya, Y. / Takusagawa, F.
History
DepositionApr 2, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: membrane-associated prostaglandin E synthase-2
B: membrane-associated prostaglandin E synthase-2
C: membrane-associated prostaglandin E synthase-2
D: membrane-associated prostaglandin E synthase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,40816
Polymers132,5994
Non-polymers1,80912
Water1,58588
1
A: membrane-associated prostaglandin E synthase-2
B: membrane-associated prostaglandin E synthase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,2048
Polymers66,3002
Non-polymers9056
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-39 kcal/mol
Surface area23870 Å2
MethodPISA
2
C: membrane-associated prostaglandin E synthase-2
D: membrane-associated prostaglandin E synthase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,2048
Polymers66,3002
Non-polymers9056
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-39 kcal/mol
Surface area23870 Å2
MethodPISA
3
A: membrane-associated prostaglandin E synthase-2
B: membrane-associated prostaglandin E synthase-2
C: membrane-associated prostaglandin E synthase-2
D: membrane-associated prostaglandin E synthase-2
hetero molecules

A: membrane-associated prostaglandin E synthase-2
B: membrane-associated prostaglandin E synthase-2
C: membrane-associated prostaglandin E synthase-2
D: membrane-associated prostaglandin E synthase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)268,81732
Polymers265,1988
Non-polymers3,61824
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area26250 Å2
ΔGint-192 kcal/mol
Surface area89160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.24, 122.83, 111.53
Angle α, β, γ (deg.)90.0, 110.6, 90.0
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
membrane-associated prostaglandin E synthase-2


Mass: 33149.809 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca fascicularis (crab-eating macaque)
Tissue: brain / Production host: Escherichia coli (E. coli) / References: UniProt: Q9N0A4, prostaglandin-E synthase
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-IMN / INDOMETHACIN


Mass: 357.788 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H16ClNO4 / Comment: medication, antiinflammatory*YM
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.77 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Ammonia sulfate, sodium acetate, indomethacin, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.99108 Å
DetectorDetector: CCD / Date: Aug 10, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99108 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. all: 47852 / Num. obs: 47852 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.6→2.7 Å / % possible all: 84

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Processing

Software
NameVersionClassification
APS19BMdata collection
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.6→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.251 4812 RANDOM
Rwork0.214 --
all0.215 47852 -
obs0.215 47852 -
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8856 0 120 88 9064
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d12.2

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