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- PDB-3o22: Structure-function analysis of human L-Prostaglandin D Synthase b... -

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Basic information

Entry
Database: PDB / ID: 3o22
TitleStructure-function analysis of human L-Prostaglandin D Synthase bound with fatty acid
ComponentsProstaglandin-H2 D-isomerase
KeywordsISOMERASE / Lipocalin / prostaglandin synthase
Function / homology
Function and homology information


prostaglandin-D synthase / Transcriptional regulation of testis differentiation / prostaglandin-D synthase activity / 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 / Transcriptional regulation of testis differentiation / prostaglandin-D synthase activity / 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 / rough endoplasmic reticulum / response to glucocorticoid / fatty acid binding / gene expression / nuclear membrane / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
Lipocalin / Lipocalin family conserved site / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin / Lipocalin signature. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
OLEIC ACID / PALMITIC ACID / Prostaglandin-H2 D-isomerase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsZhou, Y. / Shaw, N. / Li, Y. / Zhao, Y. / Zhang, R. / Liu, Z.-J.
CitationJournal: To be Published
Title: Structure-function analysis of human L-Prostaglandin D Synthase bound with fatty acid
Authors: Zhou, Y. / Shaw, N. / Li, Y. / Zhao, Y. / Zhang, R. / Liu, Z.-J.
History
DepositionJul 22, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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

Downloads & links

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Assembly

Deposited unit
A: Prostaglandin-H2 D-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1675
Polymers18,0891
Non-polymers1,0784
Water3,441191
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.971, 60.971, 179.460
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-289-

HOH

21A-301-

HOH

31A-322-

HOH

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Components

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


Mass: 18089.277 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 29-190 / Mutation: C65A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTGDS, PDS / Production host: Escherichia coli (E. coli) / References: UniProt: P41222, prostaglandin-D synthase
#2: Chemical ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H34O2
#3: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H32O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 2.66 Å3/Da / Density % sol: 53.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 3.8
Details: 0.1M citric acid, pH 3.8, 1.7M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 10, 2009
RadiationMonochromator: GRAPHITE / Protocol: LAUE / Monochromatic (M) / Laue (L): M / Scattering type: neutron
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. all: 40008 / Num. obs: 39672 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.4→1.45 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
CNSrefinement
PHENIX(phenix.refine: 1.6_289)refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CZU

2czu


Resolution: 1.4→30.486 Å / SU ML: 0.17 / σ(F): 0.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2205 1996 5.03 %RANDOM
Rwork0.193 ---
obs0.1944 39672 99.38 %-
all-40008 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.2 Å2 / ksol: 0.341 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.9381 Å20 Å20 Å2
2---0.9381 Å2-0 Å2
3---1.8763 Å2
Refinement stepCycle: LAST / Resolution: 1.4→30.486 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1224 0 76 191 1491
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051430
X-RAY DIFFRACTIONf_angle_d0.9891921
X-RAY DIFFRACTIONf_dihedral_angle_d15.526561
X-RAY DIFFRACTIONf_chiral_restr0.071203
X-RAY DIFFRACTIONf_plane_restr0.004246
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.4-1.45010.18681710.17083719100
1.4501-1.50810.20022170.1644364799
1.5081-1.57680.24042030.1589366199
1.5768-1.65990.20842300.1567365699
1.6599-1.76390.18731810.15643728100
1.7639-1.90010.19111840.1603374999
1.9001-2.09120.17821970.1535374499
2.0912-2.39370.19022080.1687378699
2.3937-3.01540.2212030.20563865100
3.0154-30.49270.24032020.21314121100

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