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- PDB-4os0: Three-dimensional structure of the C65A-W54F double mutant of Hum... -

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Basic information

Entry
Database: PDB / ID: 4os0
TitleThree-dimensional structure of the C65A-W54F double 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: 1.75 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 1.3Nov 20, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)41,9572
Polymers41,9572
Non-polymers00
Water1,892105
1
A: Prostaglandin-H2 D-isomerase


Theoretical massNumber of molelcules
Total (without water)20,9791
Polymers20,9791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Prostaglandin-H2 D-isomerase


Theoretical massNumber of molelcules
Total (without water)20,9791
Polymers20,9791
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)41,9572
Polymers41,9572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area2050 Å2
ΔGint-11 kcal/mol
Surface area16060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.622, 45.870, 48.260
Angle α, β, γ (deg.)69.40, 77.67, 65.32
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: 20978.680 Da / Num. of mol.: 2 / Mutation: C65A, W54F
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.: 105 / 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: 1.86 Å3/Da / Density % sol: 33.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 02.M Na/K Tartrate, 0.1M Na acetate, 2.0M Ammonium sulphate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 30, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.75→45.04 Å / Num. all: 30525 / Num. obs: 29286 / % possible obs: 95.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 10
Reflection shellResolution: 1.75→1.85 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.352 / Mean I/σ(I) obs: 3.4 / % possible all: 95

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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: 1.75→45.036 Å / SU ML: 0.2 / σ(F): 1.96 / Phase error: 26.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2328 1470 5.03 %
Rwork0.1958 --
obs0.1978 29212 95.7 %
all-30525 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→45.036 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2548 0 0 105 2653
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042606
X-RAY DIFFRACTIONf_angle_d0.9443518
X-RAY DIFFRACTIONf_dihedral_angle_d15.349954
X-RAY DIFFRACTIONf_chiral_restr0.068382
X-RAY DIFFRACTIONf_plane_restr0.004454
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.80650.30591180.24612484X-RAY DIFFRACTION94
1.8065-1.87110.25561260.22722483X-RAY DIFFRACTION94
1.8711-1.9460.27021160.21312496X-RAY DIFFRACTION94
1.946-2.03450.31251280.20512445X-RAY DIFFRACTION93
2.0345-2.14180.24861260.20782554X-RAY DIFFRACTION96
2.1418-2.2760.23821530.20662522X-RAY DIFFRACTION96
2.276-2.45170.25581290.21632507X-RAY DIFFRACTION95
2.4517-2.69840.24281550.21092564X-RAY DIFFRACTION97
2.6984-3.08880.27241290.21122532X-RAY DIFFRACTION97
3.0888-3.89120.2231340.17892591X-RAY DIFFRACTION98
3.8912-45.05090.19341560.17512564X-RAY DIFFRACTION98
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)
12.7628-0.88330.80483.7995-0.24452.28430.0253-0.30710.02340.42490.0142-0.0949-0.04530.0463-0.03430.1854-0.0075-0.00150.1736-0.0120.1357-0.3409-0.07831.1827
23.42320.05460.60763.28590.33522.77020.03710.448-0.0194-0.4828-0.02220.0527-0.1242-0.0118-0.01170.18420.0090.00530.17950.00090.1096-26.4154-18.4494-17.9191
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 27:189 OR RESID 201:245 ) ) OR ( CHAIN B AND RESID 201:202 )A27 - 189
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 27:189 OR RESID 201:245 ) ) OR ( CHAIN B AND RESID 201:202 )A201 - 245
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 27:189 OR RESID 201:245 ) ) OR ( CHAIN B AND RESID 201:202 )B201 - 202
4X-RAY DIFFRACTION2( CHAIN B AND ( RESID 27:189 OR RESID 203:260 ) )B27 - 189
5X-RAY DIFFRACTION2( CHAIN B AND ( RESID 27:189 OR RESID 203:260 ) )B203 - 260

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