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- PDB-4os3: Three-dimensional structure of the C65A-W112F double mutant of Hu... -

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Basic information

Entry
Database: PDB / ID: 4os3
TitleThree-dimensional structure of the C65A-W112F 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 / response to glucocorticoid / rough endoplasmic reticulum / 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 / 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: 1.4 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 1.3Oct 30, 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

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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
Water1,56787
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 area2090 Å2
ΔGint-10 kcal/mol
Surface area16140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.250, 46.250, 47.780
Angle α, β, γ (deg.)68.89, 77.15, 65.17
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, 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.: 87 / 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: 1.87 Å3/Da / Density % sol: 34.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.2M 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: 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: 1.4→26.08 Å / Num. all: 60074 / Num. obs: 57481 / % possible obs: 95.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.9 % / Rmerge(I) obs: 0.031 / Net I/σ(I): 13.2
Reflection shellResolution: 1.4→1.48 Å / % possible all: 94.4

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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: 1.4→20.011 Å / SU ML: 0.16 / σ(F): 2.01 / Phase error: 24.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2456 2911 5.06 %
Rwork0.2206 --
obs0.2219 57479 95.71 %
all-60074 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→20.011 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2539 0 0 87 2626
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082598
X-RAY DIFFRACTIONf_angle_d1.193508
X-RAY DIFFRACTIONf_dihedral_angle_d14.758951
X-RAY DIFFRACTIONf_chiral_restr0.082381
X-RAY DIFFRACTIONf_plane_restr0.007453
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.42290.31071170.27942498X-RAY DIFFRACTION94
1.4229-1.44750.31851440.2752633X-RAY DIFFRACTION94
1.4475-1.47380.31851370.252527X-RAY DIFFRACTION95
1.4738-1.50210.28091380.24422563X-RAY DIFFRACTION95
1.5021-1.53280.25561360.22942609X-RAY DIFFRACTION95
1.5328-1.56610.26721540.23642574X-RAY DIFFRACTION95
1.5661-1.60250.25751300.22582572X-RAY DIFFRACTION95
1.6025-1.64260.29371390.21492625X-RAY DIFFRACTION95
1.6426-1.6870.25321340.22282586X-RAY DIFFRACTION96
1.687-1.73660.23041430.22252593X-RAY DIFFRACTION96
1.7366-1.79260.23931620.21192578X-RAY DIFFRACTION96
1.7926-1.85660.2321350.2162646X-RAY DIFFRACTION96
1.8566-1.93090.19591360.20172600X-RAY DIFFRACTION96
1.9309-2.01870.19871360.20112653X-RAY DIFFRACTION97
2.0187-2.1250.25911390.21282616X-RAY DIFFRACTION97
2.125-2.2580.27461730.21662608X-RAY DIFFRACTION97
2.258-2.4320.23041370.22442661X-RAY DIFFRACTION97
2.432-2.67630.28761170.23292688X-RAY DIFFRACTION98
2.6763-3.06230.22691430.23532648X-RAY DIFFRACTION98
3.0623-3.85370.24541480.21672665X-RAY DIFFRACTION98
3.8537-20.01270.23051130.20862425X-RAY DIFFRACTION89
Refinement TLS params.Method: refined / Origin x: -13.2708 Å / Origin y: -9.283 Å / Origin z: -8.155 Å
111213212223313233
T0.121 Å20.019 Å20.0087 Å2-0.1057 Å20.0113 Å2--0.0836 Å2
L1.3608 °20.6309 °20.0924 °2-0.9068 °20.089 °2--0.2559 °2
S0.02 Å °0.0165 Å °-0.0318 Å °0.0084 Å °0.0142 Å °0.0021 Å °0.0018 Å °0.0066 Å °-0.0293 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 27:189 OR RESID 201:237 OR RESID 238:238 ) ) OR ( CHAIN B AND ( RESID 201:201 OR RESID 28:189 OR RESID 202:249 ) )A27 - 189
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 27:189 OR RESID 201:237 OR RESID 238:238 ) ) OR ( CHAIN B AND ( RESID 201:201 OR RESID 28:189 OR RESID 202:249 ) )A201 - 237
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 27:189 OR RESID 201:237 OR RESID 238:238 ) ) OR ( CHAIN B AND ( RESID 201:201 OR RESID 28:189 OR RESID 202:249 ) )A238
4X-RAY DIFFRACTION1( CHAIN A AND ( RESID 27:189 OR RESID 201:237 OR RESID 238:238 ) ) OR ( CHAIN B AND ( RESID 201:201 OR RESID 28:189 OR RESID 202:249 ) )B201
5X-RAY DIFFRACTION1( CHAIN A AND ( RESID 27:189 OR RESID 201:237 OR RESID 238:238 ) ) OR ( CHAIN B AND ( RESID 201:201 OR RESID 28:189 OR RESID 202:249 ) )B28 - 189
6X-RAY DIFFRACTION1( CHAIN A AND ( RESID 27:189 OR RESID 201:237 OR RESID 238:238 ) ) OR ( CHAIN B AND ( RESID 201:201 OR RESID 28:189 OR RESID 202:249 ) )B202 - 249

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