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- PDB-2wwp: Crystal structure of the human lipocalin-type prostaglandin D synthase -

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Basic information

Entry
Database: PDB / ID: 2wwp
TitleCrystal structure of the human lipocalin-type prostaglandin D synthase
ComponentsPROSTAGLANDIN-H2 D-ISOMERASE
KeywordsISOMERASE / CYTOPLASM / TRANSPORT / ENDOPLASMIC RETICULUM / FATTY ACID BIOSYNTHESIS / GOLGI APPARATUS / BETA-TRACE PROTEIN / LIPID SYNTHESIS
Function / homology
Function and homology information


prostaglandin-D synthase / prostaglandin-D synthase activity / Transcriptional regulation of testis differentiation / negative regulation of male germ cell proliferation / prostanoid biosynthetic process / regulation of circadian sleep/wake cycle, sleep / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / retinoid binding / prostaglandin biosynthetic process / mast cell degranulation ...prostaglandin-D synthase / prostaglandin-D synthase activity / Transcriptional regulation of testis differentiation / negative regulation of male germ cell proliferation / prostanoid biosynthetic process / regulation of circadian sleep/wake cycle, sleep / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / retinoid binding / prostaglandin biosynthetic process / mast cell degranulation / rough endoplasmic reticulum / response to glucocorticoid / fatty acid binding / nuclear membrane / gene expression / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
Lipocalin / Lipocalin family conserved site / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin beta-barrel core domain / Calycin / Lipocalin / Lipocalin signature. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
THIOCYANATE ION / Prostaglandin-H2 D-isomerase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRoos, A.K. / Tresaugues, L. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. ...Roos, A.K. / Tresaugues, L. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / Johansson, I. / Kallas, A. / Karlberg, T. / Kotyenova, T. / Kotzch, A. / Kraulis, P. / Markova, N. / Moche, M. / Nielsen, T.K. / Nyman, T. / Persson, C. / Schuler, H. / Schutz, P. / Siponen, M.I. / Svensson, L. / Thorsell, A.G. / Van Den Berg, S. / Wahlberg, E. / Weigelt, J. / Welin, M. / Wisniewska, M. / Nordlund, P. / Structural Genomics Consortium (SGC)
CitationJournal: J.Lipid Res. / Year: 2013
Title: Structural and Dynamic Insights Into Substrate Binding and Catalysis of Human Lipocalin Prostaglandin D Synthase.
Authors: Lim, S.M. / Chen, D. / Teo, H. / Roos, A. / Jansson, A.E. / Nyman, T. / Tresaugues, L. / Pervushin, K. / Nordlund, P.
History
DepositionOct 26, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2014Group: Database references / Derived calculations / Version format compliance
Revision 1.2May 24, 2017Group: Structure summary
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROSTAGLANDIN-H2 D-ISOMERASE
B: PROSTAGLANDIN-H2 D-ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6836
Polymers39,4962
Non-polymers1874
Water1,964109
1
A: PROSTAGLANDIN-H2 D-ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8774
Polymers19,7481
Non-polymers1293
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PROSTAGLANDIN-H2 D-ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8062
Polymers19,7481
Non-polymers581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.400, 56.590, 73.460
Angle α, β, γ (deg.)90.00, 90.15, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-1, 0.00028, -0.00328), (-0.00028, -1, -0.00066), (-0.00328, -0.00066, 1)
Vector: 18.29032, -19.83638, -36.67587)

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Components

#1: Protein PROSTAGLANDIN-H2 D-ISOMERASE / LIPOCALIN-TYPE PROSTAGLANDIN-D SYNTHASE / GLUTATHIONE-INDEPENDENT PGD SYNTHETASE / PROSTAGLANDIN-D2 ...LIPOCALIN-TYPE PROSTAGLANDIN-D SYNTHASE / GLUTATHIONE-INDEPENDENT PGD SYNTHETASE / PROSTAGLANDIN-D2 SYNTHASE / PGD2 SYNTHASE / PGDS2 / PGDS / BETA-TRACE PROTEIN / CEREBRIN-28


Mass: 19748.145 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE / References: UniProt: P41222, prostaglandin-D synthase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 1.92 Å3/Da / Density % sol: 36 % / Description: NONE
Crystal growpH: 7 / Details: 20% PEG3350, 0.2 M SODIUM THIOCYANATE, pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9686
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 23, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2→32.65 Å / Num. obs: 20007 / % possible obs: 98.3 % / Observed criterion σ(I): 2.8 / Redundancy: 3.4 % / Biso Wilson estimate: 19.9 Å2 / Rmerge(I) obs: 0.125 / Net I/σ(I): 7.8
Reflection shellResolution: 2→2.11 Å / Redundancy: 3 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.8 / % possible all: 89.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CZT

2czt


Resolution: 2→32.65 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.909 / Cross valid method: THROUGHOUT / ESU R: 0.22 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.246 983 4.9 %RANDOM
Rwork0.208 ---
obs0.21 19007 98.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.62 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å20 Å2
2---0.16 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2→32.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2315 0 8 109 2432
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222407
X-RAY DIFFRACTIONr_bond_other_d00.021626
X-RAY DIFFRACTIONr_angle_refined_deg1.1041.9463268
X-RAY DIFFRACTIONr_angle_other_deg4.20433957
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.355303
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.64123.654104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.36115384
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8591513
X-RAY DIFFRACTIONr_chiral_restr0.0670.2360
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212686
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02517
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_it0.5991.51505
X-RAY DIFFRACTIONr_mcbond_other01.5608
X-RAY DIFFRACTIONr_mcangle_it1.14122421
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.5933902
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.6034.5843
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: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 60 -
Rwork0.256 1195 -
obs--83.39 %

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