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- PDB-4orr: Threedimensional structure of the C65A mutant of Human lipocalin-... -

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Basic information

Entry
Database: PDB / ID: 4orr
TitleThreedimensional structure of the C65A mutant of Human lipocalin-type Prostaglandin D Synthase olo-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 / 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
Chem-PE3 / Prostaglandin-H2 D-isomerase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 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 1.2Sep 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_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)21,7493
Polymers21,0181
Non-polymers7312
Water1,838102
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Prostaglandin-H2 D-isomerase
hetero molecules

A: Prostaglandin-H2 D-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4976
Polymers42,0352
Non-polymers1,4624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+1/31
Buried area4120 Å2
ΔGint-41 kcal/mol
Surface area15330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.777, 60.777, 178.766
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-401-

PE3

21A-579-

HOH

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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: 21017.717 Da / Num. of mol.: 1 / Mutation: C65A
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-PE3 / 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL / POLYETHYLENE GLYCOL


Mass: 634.751 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H58O15
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.26 Å3/Da / Density % sol: 45.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M Tris, 25% PEG 4000, 2% Ethylene glycol, pH 7.0, 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 315r / Detector: CCD / Date: Nov 21, 2008
RadiationMonochromator: Channel cut ESRF monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.4→30 Å / Num. all: 39537 / Num. obs: 39501 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 12.8 % / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 6.4 / % possible all: 99.7

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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 3O2Y

3o2y


Resolution: 1.4→28.771 Å / SU ML: 0.14 / σ(F): 1.38 / Phase error: 21.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2327 1972 5 %
Rwork0.2141 --
obs0.215 37439 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→28.771 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1259 0 45 102 1406
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041337
X-RAY DIFFRACTIONf_angle_d1.0121792
X-RAY DIFFRACTIONf_dihedral_angle_d14.167508
X-RAY DIFFRACTIONf_chiral_restr0.033190
X-RAY DIFFRACTIONf_plane_restr0.004224
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3999-1.41830.23361490.24222617X-RAY DIFFRACTION99
1.4183-1.43770.30671210.24852671X-RAY DIFFRACTION100
1.4377-1.45830.29421470.24512669X-RAY DIFFRACTION100
1.4583-1.480.22621210.24042697X-RAY DIFFRACTION100
1.48-1.50320.2661240.23212655X-RAY DIFFRACTION100
1.5032-1.52780.26111220.22182685X-RAY DIFFRACTION100
1.5278-1.55420.24421350.22842670X-RAY DIFFRACTION100
1.5542-1.58240.21911510.22062626X-RAY DIFFRACTION100
1.5824-1.61290.21181300.21912683X-RAY DIFFRACTION100
1.6129-1.64580.24881490.21952658X-RAY DIFFRACTION100
1.6458-1.68160.26451400.2262645X-RAY DIFFRACTION100
1.6816-1.72070.23311680.22482616X-RAY DIFFRACTION100
1.7207-1.76370.25551190.21752678X-RAY DIFFRACTION100
1.7637-1.81140.21731470.21592666X-RAY DIFFRACTION100
1.8114-1.86470.23961500.20742647X-RAY DIFFRACTION100
1.8647-1.92480.20431470.20882644X-RAY DIFFRACTION100
1.9248-1.99360.25761290.20262670X-RAY DIFFRACTION100
1.9936-2.07340.18861400.20612666X-RAY DIFFRACTION100
2.0734-2.16770.24971440.20732666X-RAY DIFFRACTION100
2.1677-2.2820.24081680.20342635X-RAY DIFFRACTION100
2.282-2.42490.23011340.21232657X-RAY DIFFRACTION100
2.4249-2.6120.24561390.2272649X-RAY DIFFRACTION100
2.612-2.87470.21891470.21482674X-RAY DIFFRACTION100
2.8747-3.29010.25751380.21892649X-RAY DIFFRACTION100
3.2901-4.14320.21011330.19852664X-RAY DIFFRACTION100
4.1432-28.77710.22581400.21652533X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: -16.277 Å / Origin y: 5.3446 Å / Origin z: 36.3974 Å
111213212223313233
T0.0912 Å20.0108 Å20.0185 Å2-0.1147 Å20.0082 Å2--0.1029 Å2
L1.119 °20.1065 °2-0.4623 °2-0.773 °20.0006 °2--1.2784 °2
S-0.057 Å °0.121 Å °-0.0693 Å °-0.03 Å °0.027 Å °0.0386 Å °0.0634 Å °-0.0343 Å °0.0259 Å °
Refinement TLS groupSelection details: (CHAIN A AND (RESID 28:188 OR RESID 401:402 OR RESID 501:602 ) )

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