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- PDB-5ywe: Crystal structure of hematopoietic prostaglandin D synthase apo form -

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Basic information

Entry
Database: PDB / ID: 5ywe
TitleCrystal structure of hematopoietic prostaglandin D synthase apo form
ComponentsHematopoietic prostaglandin D synthase
KeywordsTRANSFERASE / PROSTAGLANDIN D / Synthase
Function / homology
Function and homology information


prostaglandin-D synthase / prostaglandin-D synthase activity / negative regulation of male germ cell proliferation / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / Glutathione conjugation / prostaglandin biosynthetic process / prostaglandin metabolic process / glutathione transferase / glutathione transferase activity / locomotory behavior ...prostaglandin-D synthase / prostaglandin-D synthase activity / negative regulation of male germ cell proliferation / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / Glutathione conjugation / prostaglandin biosynthetic process / prostaglandin metabolic process / glutathione transferase / glutathione transferase activity / locomotory behavior / intracellular membrane-bounded organelle / calcium ion binding / magnesium ion binding / signal transduction / protein homodimerization activity / nucleoplasm / cytosol / cytoplasm
Similarity search - Function
Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. / 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 ...Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. / 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 / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.68 Å
AuthorsKamo, M. / Furubayashi, N. / Inaka, K. / Aritake, K. / Urade, Y.
CitationJournal: To Be Published
Title: Crystal structure of hematopoietic prostaglandin D synthase apo form
Authors: Inaka, K. / Furubayashi, N. / Kamo, M. / Aritake, K. / Urade, Y.
History
DepositionNov 29, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 5, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hematopoietic prostaglandin D synthase
B: Hematopoietic prostaglandin D synthase
C: Hematopoietic prostaglandin D synthase
D: Hematopoietic prostaglandin D synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,42112
Polymers92,9594
Non-polymers1,4628
Water10,395577
1
A: Hematopoietic prostaglandin D synthase
B: Hematopoietic prostaglandin D synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3027
Polymers46,4792
Non-polymers8235
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-35 kcal/mol
Surface area18660 Å2
MethodPISA
2
C: Hematopoietic prostaglandin D synthase
D: Hematopoietic prostaglandin D synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1185
Polymers46,4792
Non-polymers6393
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-34 kcal/mol
Surface area18720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.429, 48.200, 88.969
Angle α, β, γ (deg.)95.820, 90.080, 89.970
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Hematopoietic prostaglandin D synthase / H-PGDS / GST class-sigma / Glutathione S-transferase / Glutathione-dependent PGD synthase / ...H-PGDS / GST class-sigma / Glutathione S-transferase / Glutathione-dependent PGD synthase / Glutathione-requiring prostaglandin D synthase / Prostaglandin-H2 D-isomerase


Mass: 23239.637 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HPGDS, GSTS, PGDS, PTGDS2 / Production host: Escherichia coli (E. coli)
References: UniProt: O60760, prostaglandin-D synthase, glutathione transferase
#2: Chemical
ChemComp-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 577 / 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: 2.18 Å3/Da / Density % sol: 43.49 %
Crystal growTemperature: 293 K / Method: liquid diffusion / pH: 8.5
Details: 35% PEG 6000, 5 mM DTT, 2mM MgCl2, 2mM Glutathione, 2% Dioxane, 50 mM Tris-HCL, pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 17, 2014
RadiationMonochromator: Rotated-inclined double-crystal monochromator , Si (111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.68→88.51 Å / Num. obs: 71217 / % possible obs: 79.7 % / Redundancy: 3.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.035 / Rrim(I) all: 0.067 / Net I/σ(I): 12.3 / Num. measured all: 255531 / Scaling rejects: 151
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.68-1.713.50.31635900.9080.1910.3777.8
9.05-88.5140.0385580.9970.0220.04397

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation88.51 Å3 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
Aimless0.5.17data scaling
MOLREP11.0.05phasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CVD

2cvd


Resolution: 1.68→88.51 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.987 / SU ML: 0.067 / SU R Cruickshank DPI: 0.1401 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.14 / ESU R Free: 0.127
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2046 3316 4.8 %RANDOM
Rwork0.1693 ---
obs0.171 65506 76.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 72.96 Å2 / Biso mean: 20.213 Å2 / Biso min: 6.03 Å2
Baniso -1Baniso -2Baniso -3
1--0.82 Å20.22 Å2-0.01 Å2
2--0.88 Å20.25 Å2
3----0.09 Å2
Refinement stepCycle: final / Resolution: 1.68→88.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6552 0 94 577 7223
Biso mean--22.57 24.65 -
Num. residues----792
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0196810
X-RAY DIFFRACTIONr_bond_other_d0.0010.026448
X-RAY DIFFRACTIONr_angle_refined_deg1.1951.9639250
X-RAY DIFFRACTIONr_angle_other_deg0.737314824
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3115788
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.96624.217332
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.554151168
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1641540
X-RAY DIFFRACTIONr_chiral_restr0.0640.21014
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217600
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021608
LS refinement shellResolution: 1.68→1.724 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 170 -
Rwork0.206 3101 -
all-3271 -
obs--49.43 %

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