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Basic information

Entry
Database: PDB / ID: 4ory
TitleThree-dimensional structure of the C65A-K59A double mutant of Human lipocalin-type Prostaglandin D Synthase holo, second crystal 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 / MOLECULAR REPLACEMENT / Resolution: 1.8 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 1.3Sep 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
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
C: Prostaglandin-H2 D-isomerase
D: Prostaglandin-H2 D-isomerase
E: Prostaglandin-H2 D-isomerase
F: Prostaglandin-H2 D-isomerase
G: Prostaglandin-H2 D-isomerase
H: Prostaglandin-H2 D-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,12010
Polymers167,6778
Non-polymers2,4432
Water2,558142
1
A: Prostaglandin-H2 D-isomerase


Theoretical massNumber of molelcules
Total (without water)20,9601
Polymers20,9601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Prostaglandin-H2 D-isomerase


Theoretical massNumber of molelcules
Total (without water)20,9601
Polymers20,9601
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Prostaglandin-H2 D-isomerase


Theoretical massNumber of molelcules
Total (without water)20,9601
Polymers20,9601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Prostaglandin-H2 D-isomerase


Theoretical massNumber of molelcules
Total (without water)20,9601
Polymers20,9601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Prostaglandin-H2 D-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1812
Polymers20,9601
Non-polymers1,2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Prostaglandin-H2 D-isomerase


Theoretical massNumber of molelcules
Total (without water)20,9601
Polymers20,9601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Prostaglandin-H2 D-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1812
Polymers20,9601
Non-polymers1,2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Prostaglandin-H2 D-isomerase


Theoretical massNumber of molelcules
Total (without water)20,9601
Polymers20,9601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.378, 67.378, 287.673
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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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: 20959.613 Da / Num. of mol.: 8 / Mutation: C65A, K59A
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-PEU / 2,5,8,11,14,17,20,23,26,29,32,35,38,41,44,47,50,53,56,59,62,65,68,71,74,77,80-HEPTACOSAOXADOOCTACONTAN-82-OL / PEG 8000


Mass: 1221.461 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H112O28 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 1.94 Å3/Da / Density % sol: 36.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1M Na Acetate, 0.2M Ammonium sulphate, 30% PEG 2000 MME, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 25, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 117813 / Num. obs: 117470 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.2
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.061 / Mean I/σ(I) obs: 2.6 / % possible all: 100

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Processing

Software
NameVersionClassification
DNAdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4ORR

4orr


Resolution: 1.8→49.17 Å / SU ML: 0.22 / σ(F): 1.38 / Phase error: 24.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2489 5882 5.01 %
Rwork0.2079 --
obs0.21 117341 99.6 %
all-117813 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→49.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10043 0 152 142 10337
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00510436
X-RAY DIFFRACTIONf_angle_d1.01414060
X-RAY DIFFRACTIONf_dihedral_angle_d15.3673875
X-RAY DIFFRACTIONf_chiral_restr0.071503
X-RAY DIFFRACTIONf_plane_restr0.0041793
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82050.32831990.28373750X-RAY DIFFRACTION100
1.8205-1.84190.31782050.25833645X-RAY DIFFRACTION100
1.8419-1.86430.27521920.2393793X-RAY DIFFRACTION100
1.8643-1.88790.31091870.24243702X-RAY DIFFRACTION100
1.8879-1.91280.28042000.22923772X-RAY DIFFRACTION100
1.9128-1.9390.25642070.22653689X-RAY DIFFRACTION100
1.939-1.96670.28672020.23363684X-RAY DIFFRACTION100
1.9667-1.9960.31192070.23433730X-RAY DIFFRACTION100
1.996-2.02720.27642040.22043738X-RAY DIFFRACTION100
2.0272-2.06050.2521940.21943717X-RAY DIFFRACTION100
2.0605-2.0960.25291890.2113726X-RAY DIFFRACTION100
2.096-2.13410.29171940.21193725X-RAY DIFFRACTION100
2.1341-2.17520.26431890.21683762X-RAY DIFFRACTION100
2.1752-2.21960.25931970.21943681X-RAY DIFFRACTION100
2.2196-2.26780.25071970.22273752X-RAY DIFFRACTION100
2.2678-2.32060.25261670.22223795X-RAY DIFFRACTION100
2.3206-2.37860.26782000.21563668X-RAY DIFFRACTION100
2.3786-2.44290.26021990.2223752X-RAY DIFFRACTION100
2.4429-2.51480.28112010.23093706X-RAY DIFFRACTION100
2.5148-2.5960.27452130.22293766X-RAY DIFFRACTION100
2.596-2.68870.28242020.2253707X-RAY DIFFRACTION100
2.6887-2.79640.28151740.21453754X-RAY DIFFRACTION100
2.7964-2.92360.25671830.22953719X-RAY DIFFRACTION100
2.9236-3.07780.29032180.23483725X-RAY DIFFRACTION100
3.0778-3.27060.2161810.21053742X-RAY DIFFRACTION100
3.2706-3.5230.24181950.19963733X-RAY DIFFRACTION100
3.523-3.87740.24621990.18313701X-RAY DIFFRACTION100
3.8774-4.43820.20142180.16743714X-RAY DIFFRACTION100
4.4382-5.59040.19742020.17533714X-RAY DIFFRACTION99
5.5904-49.18840.25161670.21723397X-RAY DIFFRACTION90
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)
11.05010.3906-0.04931.36760.44740.76660.0461-0.22290.27720.15180.0377-0.18420.06530.0358-0.06450.13140.0035-0.00880.2815-0.05980.3137-29.120423.8514-2.9438
20.88330.1388-0.23460.21720.09080.6767-0.04580.45320.1559-0.0336-0.07050.17810.1803-0.289-0.05170.0618-0.0390.02831.3185-0.22620.4226-64.936525.54772.3681
31.32430.26630.09740.73370.08051.117-0.12690.42620.0815-0.24970.12970.17040.0288-0.4310.00130.2776-0.0499-0.01840.4572-0.02720.2765-26.466818.7847-39.2426
40.43050.329-0.11460.34870.06171.175-0.0691-0.3840.15140.09740.13980.00540.07940.3631-0.06710.4185-0.1315-0.01540.96490.03740.4651-62.054417.7553-33.3183
50.93170.14160.05780.4509-0.18270.4691-0.0435-0.4477-0.14980.1758-0.1255-0.0994-0.0680.20760.03490.008-0.01420.05790.45470.04970.1966-14.3376-7.02820.9172
60.82020.00240.11090.5896-0.05410.9972-0.10120.0636-0.11470.00290.05990.0265-0.06470.00460.0350.1252-0.00860.02750.2720.01350.166121.1009-6.53556.6159
71.0340.1374-0.14170.756-0.18161.4279-0.031-0.0947-0.09190.02350.01440.0097-0.11680.03990.01750.1102-0.0210.02160.2381-0.03570.1672-15.8498-12.2445-34.9292
80.78580.00440.11870.19110.09280.6517-0.02480.5807-0.2066-0.1108-0.08990.071-0.0931-0.0760.04040.15440.03410.01650.6472-0.12950.287819.4912-11.726-28.2516
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 29:187 OR RESID 201:225 ) )A29 - 187
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 29:187 OR RESID 201:225 ) )A201 - 225
3X-RAY DIFFRACTION2( CHAIN B AND RESID 29:189 )B29 - 189
4X-RAY DIFFRACTION3( CHAIN C AND ( RESID 29:188 OR RESID 201:207 ) )C29 - 188
5X-RAY DIFFRACTION3( CHAIN C AND ( RESID 29:188 OR RESID 201:207 ) )C201 - 207
6X-RAY DIFFRACTION4( CHAIN D AND ( RESID 30:186 OR RESID 201:202 ) )D30 - 186
7X-RAY DIFFRACTION4( CHAIN D AND ( RESID 30:186 OR RESID 201:202 ) )D201 - 202
8X-RAY DIFFRACTION5( CHAIN E AND ( RESID 29:188 OR RESID 301:331 ) )E29 - 188
9X-RAY DIFFRACTION5( CHAIN E AND ( RESID 29:188 OR RESID 301:331 ) )E301 - 331
10X-RAY DIFFRACTION6( CHAIN H AND RESID 201:202 ) OR ( CHAIN F AND ( RESID 23:189 OR RESID 201:231 ) )H201 - 202
11X-RAY DIFFRACTION6( CHAIN H AND RESID 201:202 ) OR ( CHAIN F AND ( RESID 23:189 OR RESID 201:231 ) )F23 - 189
12X-RAY DIFFRACTION6( CHAIN H AND RESID 201:202 ) OR ( CHAIN F AND ( RESID 23:189 OR RESID 201:231 ) )F201 - 231
13X-RAY DIFFRACTION7( CHAIN H AND RESID 203:203 ) OR ( CHAIN G AND ( RESID 23:188 OR RESID 301:326 ) )H203
14X-RAY DIFFRACTION7( CHAIN H AND RESID 203:203 ) OR ( CHAIN G AND ( RESID 23:188 OR RESID 301:326 ) )G23 - 188
15X-RAY DIFFRACTION7( CHAIN H AND RESID 203:203 ) OR ( CHAIN G AND ( RESID 23:188 OR RESID 301:326 ) )G301 - 326
16X-RAY DIFFRACTION8( CHAIN H AND ( RESID 29:186 OR RESID 204:219 ) ) OR ( CHAIN F AND RESID 232:232 )H29 - 186
17X-RAY DIFFRACTION8( CHAIN H AND ( RESID 29:186 OR RESID 204:219 ) ) OR ( CHAIN F AND RESID 232:232 )H204 - 219
18X-RAY DIFFRACTION8( CHAIN H AND ( RESID 29:186 OR RESID 204:219 ) ) OR ( CHAIN F AND RESID 232:232 )F232

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