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- PDB-4imo: Crystal structure of wild type human Lipocalin PGDS in complex wi... -

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Basic information

Entry
Database: PDB / ID: 4imo
TitleCrystal structure of wild type human Lipocalin PGDS in complex with substrate analog U44069
ComponentsLipocalin-type prostaglandin-D synthase
KeywordsISOMERASE / Beta barrel / Endoplasmic reticulum
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 / regulation of circadian sleep/wake cycle, sleep / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / cyclooxygenase pathway / 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 / regulation of circadian sleep/wake cycle, sleep / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / cyclooxygenase pathway / retinoid binding / prostaglandin biosynthetic process / mast cell degranulation / response to glucocorticoid / rough endoplasmic reticulum / 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
Chem-PWZ / THIOCYANATE ION / Prostaglandin-H2 D-isomerase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsLim, S.M. / Chen, D. / Teo, H. / Roos, A. / Nyman, T. / Tresaugues, L. / Pervushin, K. / Nordlund, P.
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
DepositionJan 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Database references
Revision 1.2Sep 20, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Lipocalin-type prostaglandin-D synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5655
Polymers19,7481
Non-polymers8174
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.240, 56.380, 72.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Lipocalin-type prostaglandin-D synthase / Beta-trace protein / Cerebrin-28 / Glutathione-independent PGD synthase / Prostaglandin-H2 D- ...Beta-trace protein / Cerebrin-28 / Glutathione-independent PGD synthase / Prostaglandin-H2 D-isomerase / Prostaglandin-D2 synthase / PGD2 synthase / PGDS / PGDS2


Mass: 19748.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDS, PTGDS / Plasmid: pNIC-CH4 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta BL21 / References: UniProt: P41222, prostaglandin-D synthase
#2: Chemical ChemComp-PWZ / (5E)-7-{(1R,4S,5S,6R)-5-[(1E,3S)-3-hydroxyoct-1-en-1-yl]-2-oxabicyclo[2.2.1]hept-6-yl}hept-5-enoic acid


Mass: 350.492 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H34O4
#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.: 82 / 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: 1.89 Å3/Da / Density % sol: 34.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M potassium thiocyanate, 30% PEG MME 2000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 198 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.97622 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 30, 2011
RadiationMonochromator: LN2-cooled, fixed-exit double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 1.88→36.49 Å / Num. all: 12735 / Num. obs: 12735 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 23.5 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 7.4
Reflection shellResolution: 1.88→1.98 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 2.8 / Num. unique all: 1826 / Rsym value: 0.274 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERMRphasing
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CZT

2czt


Resolution: 1.88→36.49 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.918 / SU B: 3.34 / SU ML: 0.103 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / ESU R: 0.165 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24154 620 4.9 %RANDOM
Rwork0.18911 ---
obs0.19174 12074 99.98 %-
all-12074 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.509 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å20 Å2
2---0.71 Å20 Å2
3---0.55 Å2
Refinement stepCycle: LAST / Resolution: 1.88→36.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1215 0 56 82 1353
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.021324
X-RAY DIFFRACTIONr_bond_other_d0.0070.021240
X-RAY DIFFRACTIONr_angle_refined_deg1.5081.9871792
X-RAY DIFFRACTIONr_angle_other_deg1.4783.0162877
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3165164
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.65323.45555
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.99415214
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.963158
X-RAY DIFFRACTIONr_chiral_restr0.0820.2198
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211475
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02315
LS refinement shellResolution: 1.88→1.929 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 45 -
Rwork0.192 869 -
obs--100 %

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