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- PDB-4os8: Three-dimensional structure of the C65A-W54F-W112F triple mutant ... -

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Basic information

Entry
Database: PDB / ID: 4os8
TitleThree-dimensional structure of the C65A-W54F-W112F triple mutant of Human lipocalin-type Prostaglandin D Synthase apo-form
ComponentsProstaglandin-H2 D-isomerase
KeywordsISOMERASE / LIPOCALIN-TYPE PROSTAGLANDIN-D SYNTHASE
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
Prostaglandin-H2 D-isomerase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.69 Å
AuthorsPerduca, M. / Bovi, M. / Bertinelli, M. / Bertini, E. / Destefanis, L. / Carrizo, M.E. / Capaldi, S. / Monaco, H.L.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: High-resolution structures of mutants of residues that affect access to the ligand-binding cavity of human lipocalin-type prostaglandin D synthase.
Authors: Perduca, M. / Bovi, M. / Bertinelli, M. / Bertini, E. / Destefanis, L. / Carrizo, M.E. / Capaldi, S. / Monaco, H.L.
History
DepositionFeb 12, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2014Group: Database references
Revision 1.2Dec 17, 2014Group: Structure summary
Revision 1.3Feb 26, 2020Group: Data collection / Database references / Category: reflns / reflns_shell / struct_ref_seq_dif
Item: _reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs / _struct_ref_seq_dif.details
Revision 1.4Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Prostaglandin-H2 D-isomerase
B: Prostaglandin-H2 D-isomerase


Theoretical massNumber of molelcules
Total (without water)41,8792
Polymers41,8792
Non-polymers00
Water2,432135
1
A: Prostaglandin-H2 D-isomerase


Theoretical massNumber of molelcules
Total (without water)20,9401
Polymers20,9401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Prostaglandin-H2 D-isomerase


Theoretical massNumber of molelcules
Total (without water)20,9401
Polymers20,9401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Prostaglandin-H2 D-isomerase

B: Prostaglandin-H2 D-isomerase


Theoretical massNumber of molelcules
Total (without water)41,8792
Polymers41,8792
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area2020 Å2
ΔGint-7 kcal/mol
Surface area16190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.510, 46.620, 47.890
Angle α, β, γ (deg.)69.14, 77.10, 64.81
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 20939.645 Da / Num. of mol.: 2 / Mutation: C65A, W54F, W112F
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.91 Å3/Da / Density % sol: 35.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Na Acetate, 2.0M Ammonium sulphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 30, 2013
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.69→33.73 Å / Num. all: 34752 / Num. obs: 33458 / % possible obs: 96.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.2 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.6
Reflection shellResolution: 1.69→1.78 Å / Rmerge(I) obs: 0.205 / % possible all: 94.8

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Processing

Software
NameVersionClassification
DNAdata collection
Cootmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.69→33.73 Å / SU ML: 0.18 / σ(F): 2.05 / Phase error: 22.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2324 1688 5.05 %
Rwork0.1943 --
obs0.1963 33458 96.29 %
all-34752 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.69→33.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2533 0 0 135 2668
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042590
X-RAY DIFFRACTIONf_angle_d0.9033494
X-RAY DIFFRACTIONf_dihedral_angle_d14.492951
X-RAY DIFFRACTIONf_chiral_restr0.065381
X-RAY DIFFRACTIONf_plane_restr0.004453
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.689-1.73870.24471070.21052623X-RAY DIFFRACTION95
1.7387-1.79480.22771400.2032625X-RAY DIFFRACTION95
1.7948-1.8590.27571320.19922642X-RAY DIFFRACTION96
1.859-1.93340.26941520.18692637X-RAY DIFFRACTION96
1.9334-2.02140.24651430.18622632X-RAY DIFFRACTION96
2.0214-2.12790.25721250.19532660X-RAY DIFFRACTION96
2.1279-2.26120.21941570.19182650X-RAY DIFFRACTION96
2.2612-2.43580.22631560.19872646X-RAY DIFFRACTION97
2.4358-2.68080.22541380.20152686X-RAY DIFFRACTION97
2.6808-3.06850.27751520.20772636X-RAY DIFFRACTION97
3.0685-3.86510.17311300.19152718X-RAY DIFFRACTION98
3.8651-33.74030.20651560.1742615X-RAY DIFFRACTION96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.70210.0496-0.02470.73220.08360.60120.0574-0.16410.00620.1421-0.0106-0.0333-0.01970.05260.03060.0443-0.00360.00340.0486-0.00440.0149-0.1981-0.30371.2868
20.9363-0.06040.040.57150.08480.36140.00680.1643-0.0558-0.14320.01530.0252-0.0412-0.0260.01650.0409-0.0097-0.00440.03630.0070.0237-27.0374-18.7348-17.6191
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 27:189 OR RESID 201:271 ) ) OR ( CHAIN B AND RESID 201:204 )A27 - 189
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 27:189 OR RESID 201:271 ) ) OR ( CHAIN B AND RESID 201:204 )A201 - 271
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 27:189 OR RESID 201:271 ) ) OR ( CHAIN B AND RESID 201:204 )B201 - 204
4X-RAY DIFFRACTION2( CHAIN B AND ( RESID 27:188 OR RESID 205:264 ) )B27 - 188
5X-RAY DIFFRACTION2( CHAIN B AND ( RESID 27:188 OR RESID 205:264 ) )B205 - 264

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