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- PDB-1pd2: CRYSTAL STRUCTURE OF HEMATOPOIETIC PROSTAGLANDIN D SYNTHASE COMPL... -

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Basic information

Entry
Database: PDB / ID: 1pd2
TitleCRYSTAL STRUCTURE OF HEMATOPOIETIC PROSTAGLANDIN D SYNTHASE COMPLEX WITH GLUTATHIONE
ComponentsHEMATOPOIETIC PROSTAGLANDIN D SYNTHASE
KeywordsLIGASE / HEMATOPOIETIC PROSTAGLANDIN D SYNTHASE / PGDS / GST / SIGMA-CLASS GST
Function / homology
Function and homology information


Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / Glutathione conjugation / prostaglandin-D synthase / prostaglandin-D synthase activity / negative regulation of male germ cell proliferation / response to selenium ion / response to nematode / prostaglandin biosynthetic process / prostaglandin metabolic process / glutathione transferase ...Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / Glutathione conjugation / prostaglandin-D synthase / prostaglandin-D synthase activity / negative regulation of male germ cell proliferation / response to selenium ion / response to nematode / prostaglandin biosynthetic process / prostaglandin metabolic process / glutathione transferase / glutathione transferase activity / glutathione metabolic process / calcium ion binding / magnesium ion binding / protein homodimerization activity / cytoplasm
Similarity search - Function
Glutathione S-transferase, C-terminal domain / : / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-terminal domain profile. ...Glutathione S-transferase, C-terminal domain / : / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GLUTATHIONE / Hematopoietic prostaglandin D synthase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.3 Å
AuthorsMiyano, M. / Ago, H.
Citation
Journal: Cell(Cambridge,Mass.) / Year: 1997
Title: Cloning and crystal structure of hematopoietic prostaglandin D synthase.
Authors: Kanaoka, Y. / Ago, H. / Inagaki, E. / Nanayama, T. / Miyano, M. / Kikuno, R. / Fujii, Y. / Eguchi, N. / Toh, H. / Urade, Y. / Hayaishi, O.
#1: Journal: Cell(Cambridge,Mass.) / Year: 1999
Title: Erratum. Cloning and Crystal Structure of Hematopoietic Prostaglandin D Synthase
Authors: Kanaoka, Y. / Ago, H. / Inagaki, E. / Nanayama, T. / Miyano, M. / Kikuno, R. / Fujii, Y. / Eguchi, N. / Toh, H. / Urade, Y. / Hayaishi, O.
History
DepositionDec 14, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Oct 13, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 14, 2011Group: Non-polymer description
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Dec 27, 2023Group: 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
1: HEMATOPOIETIC PROSTAGLANDIN D SYNTHASE
2: HEMATOPOIETIC PROSTAGLANDIN D SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2634
Polymers46,6482
Non-polymers6152
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-26 kcal/mol
Surface area18730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.500, 56.500, 233.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.969084, 0.134643, 0.206756), (-0.151277, -0.986232, -0.066794), (0.194916, -0.096007, 0.97611)
Vector: -4.0292, 100.8681, 4.9353)

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Components

#1: Protein HEMATOPOIETIC PROSTAGLANDIN D SYNTHASE / HPGDS / SPLEEN TYPE PGDS / GLUTATHIONE DEPENDENT PGDS


Mass: 23323.943 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cellular location: CYTOPLASM / Organ: SPLEEN / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASMIC / Gene (production host): DE3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: O35543, prostaglandin-D synthase
#2: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.2 Å3/Da / Density % sol: 46.62 %
Crystal growDetails: VAPOR DIFFUSION METHOD RESERVOIR SOLUTION: 18% (W/V) PEG 6K, 100 MM AMMONIUM CITRATE 5MM CACL2, 10MM DTT, 2% (V/V) 1,4-DIOXANE PROTEIN SOLUTION: 7.3 MG/ML PROTEIN (50 MM TRIS-HCL [PH 7.5]) ...Details: VAPOR DIFFUSION METHOD RESERVOIR SOLUTION: 18% (W/V) PEG 6K, 100 MM AMMONIUM CITRATE 5MM CACL2, 10MM DTT, 2% (V/V) 1,4-DIOXANE PROTEIN SOLUTION: 7.3 MG/ML PROTEIN (50 MM TRIS-HCL [PH 7.5]) EACH 4 UL WAS MIXED FOR DROPLET
Components of the solutions
IDNameCrystal-IDSol-ID
17.3 MG/ML PROTEIN (50 MM TRIS-HCL [PH 7.5})11
210% (W/V) PEG 6K12
3100 MM AMMONIUM CITRATE12
45MM CACL212
510MM DTT12
62% (V/V) 1,4-DIOXANE12
Crystal grow
*PLUS
Temperature: 22.5 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17.3 mg/mlprotein1drop
250 mMTris-HCl1drop
310 mMGSH1drop
418 %(w/v)PEG60001reservoir
5100 mMammonium citrate1reservoir
65 mM1reservoirCaCl2
710 mMdithiothreitol1reservoir
82 %(v/v)1,4-dioxane1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorType: RIGAKU / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. obs: 77899 / % possible obs: 95.1 % / Redundancy: 4 % / Rmerge(I) obs: 0.085

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Processing

Software
NameVersionClassification
WEISdata scaling
ROTAVATAdata reduction
PHASESphasing
X-PLOR3.1refinement
WEISdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
RefinementMethod to determine structure: MIRAS / Resolution: 2.3→6 Å / Cross valid method: PROCHECK / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.289 -10 %RANDOM
Rwork0.204 ---
obs-17811 95.1 %-
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 2.3→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3296 0 40 99 3435
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.613
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 2.3→2.4 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3278 -5 %
Rwork0.2776 1852 -
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 6 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor obs: 0.204
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 2.4 Å / % reflection Rfree: 5 %

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