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- PDB-2pbj: GSH-heme bound microsomal prostaglandin E synthase -

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Basic information

Entry
Database: PDB / ID: 2pbj
TitleGSH-heme bound microsomal prostaglandin E synthase
ComponentsProstaglandin E synthase 2
KeywordsISOMERASE / LYASE / Prostaglandin E synthase / GSH-heme bound enzyme / Dual function enzyme
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
GLUTATHIONE / PROTOPORPHYRIN IX CONTAINING FE / Prostaglandin E synthase 2
Similarity search - Component
Biological speciesMacaca fascicularis (crab-eating macaque)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsTakusagawa, F. / Yamada, T.
CitationJournal: Biochemistry / Year: 2007
Title: PGH2 degradation pathway catalyzed by GSH-heme complex bound microsomal prostaglandin E2 synthase type 2: the first example of a dual-function enzyme.
Authors: Yamada, T. / Takusagawa, F.
History
DepositionMar 28, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 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: Prostaglandin E synthase 2
B: Prostaglandin E synthase 2
C: Prostaglandin E synthase 2
D: Prostaglandin E synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,43616
Polymers132,5994
Non-polymers3,83712
Water3,009167
1
A: Prostaglandin E synthase 2
B: Prostaglandin E synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2188
Polymers66,3002
Non-polymers1,9196
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Prostaglandin E synthase 2
D: Prostaglandin E synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2188
Polymers66,3002
Non-polymers1,9196
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.000, 122.490, 110.970
Angle α, β, γ (deg.)90.00, 111.00, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Prostaglandin E synthase 2


Mass: 33149.809 Da / Num. of mol.: 4 / Fragment: N-terminal truncated protein
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca fascicularis (crab-eating macaque)
Gene: mPGES-2 / Plasmid: pTrc-HisA-mPGES-2 / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: UniProt: Q9N0A4, prostaglandin-E synthase
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical
ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N3O6S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 3.04 Å3/Da / Density % sol: 59.5 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 5.5
Details: 1.7 M ammonium sulfate, 100 mM sodium acetate, pH 5.5, VAPOR DIFFUSION, temperature 295K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jan 1, 2007 / Details: Confocal
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 35201 / Num. obs: 35201 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.074

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→20 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.269 3400 -
Rwork0.242 --
obs0.242 35201 100 %
all-35201 -
Refine analyzeLuzzati coordinate error obs: 0.039 Å
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8856 0 256 167 9279
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.15

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