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- PDB-4orx: Three-dimensional structure of the C65A-K59A double mutant of Hum... -

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Basic information

Entry
Database: PDB / ID: 4orx
TitleThree-dimensional structure of the C65A-K59A double mutant of Human lipocalin-type Prostaglandin D Synthase holo-form
ComponentsProstaglandin-H2 D-isomerase
KeywordsISOMERASE / LIPOCALIN-TYPE PROSTAGLANDIN-D SYNTHASE / PEG
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: 1.6 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 1.2Oct 8, 2014Group: Structure summary
Revision 1.3Dec 17, 2014Group: Structure summary
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)43,2374
Polymers41,9192
Non-polymers1,3182
Water1,910106
1
A: Prostaglandin-H2 D-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0562
Polymers20,9601
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 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
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-42 kcal/mol
Surface area15110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.970, 90.970, 36.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
DetailsA dimer in the asymmetric unit

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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.: 2 / 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: 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.: 1 / Source method: obtained synthetically / Formula: C55H112O28 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 1.81 Å3/Da / Density % sol: 31.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30% PEG 4000, 0.2M 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: 1.6→28.77 Å / Num. all: 40121 / Num. obs: 39985 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.3 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 18.8
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 5.9 / % possible all: 100

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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: 1.6→28.581 Å / SU ML: 0.16 / σ(F): 1.36 / Phase error: 22.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2261 2008 5.02 %RANDOM
Rwork0.1988 ---
obs0.2002 39967 99.64 %-
all-40121 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→28.581 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2482 0 81 106 2669
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042621
X-RAY DIFFRACTIONf_angle_d0.9223516
X-RAY DIFFRACTIONf_dihedral_angle_d15.207995
X-RAY DIFFRACTIONf_chiral_restr0.063370
X-RAY DIFFRACTIONf_plane_restr0.003442
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.26951260.22632714X-RAY DIFFRACTION100
1.64-1.68440.26751440.22212678X-RAY DIFFRACTION100
1.6844-1.73390.25971570.21642674X-RAY DIFFRACTION100
1.7339-1.78990.2871370.2192696X-RAY DIFFRACTION100
1.7899-1.85390.23761330.21462745X-RAY DIFFRACTION100
1.8539-1.92810.25681430.19792703X-RAY DIFFRACTION100
1.9281-2.01580.24011500.19512686X-RAY DIFFRACTION100
2.0158-2.1220.21221560.19722692X-RAY DIFFRACTION100
2.122-2.25490.24881340.20162704X-RAY DIFFRACTION100
2.2549-2.4290.22941340.21192763X-RAY DIFFRACTION100
2.429-2.67320.25381600.21532703X-RAY DIFFRACTION100
2.6732-3.05970.23211350.21082761X-RAY DIFFRACTION100
3.0597-3.85340.20351420.18692743X-RAY DIFFRACTION100
3.8534-28.58550.19651570.182697X-RAY DIFFRACTION95
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)
11.15410.2961-0.21522.0656-0.42371.07920.02240.00050.0365-0.1521-0.02240.23880.0471-0.03020.00440.0756-0.0009-0.03380.0974-0.0010.069124.7295-43.8342-0.5893
22.6719-0.2088-1.07281.38850.21081.00870.1573-0.04440.10350.0759-0.08660.068-0.09540.02610.03290.1206-0.01080.07070.156-0.03780.16311.3155-68.04813.145
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 29:187 OR RESID 301:362 ) ) OR ( CHAIN B AND RESID 301:301 )A29 - 187
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 29:187 OR RESID 301:362 ) ) OR ( CHAIN B AND RESID 301:301 )A301 - 362
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 29:187 OR RESID 301:362 ) ) OR ( CHAIN B AND RESID 301:301 )B301
4X-RAY DIFFRACTION2( CHAIN B AND ( RESID 29:187 OR RESID 302:344 ) )B29 - 187
5X-RAY DIFFRACTION2( CHAIN B AND ( RESID 29:187 OR RESID 302:344 ) )B302 - 344

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