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- PDB-4oru: Three-dimensional structure of the C65A mutant of Human lipocalin... -

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Basic information

Entry
Database: PDB / ID: 4oru
TitleThree-dimensional structure of the C65A mutant of Human lipocalin-type Prostaglandin D Synthase holo-form second space group
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
Prostaglandin-H2 D-isomerase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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 1.4Nov 6, 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
B: Prostaglandin-H2 D-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2573
Polymers42,0352
Non-polymers1,2211
Water1,51384
1
A: Prostaglandin-H2 D-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2392
Polymers21,0181
Non-polymers1,2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Prostaglandin-H2 D-isomerase


Theoretical massNumber of molelcules
Total (without water)21,0181
Polymers21,0181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-28 kcal/mol
Surface area15030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.130, 91.130, 36.810
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: 21017.717 Da / Num. of mol.: 2 / 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-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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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

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Sample preparation

CrystalDensity Matthews: 1.82 Å3/Da / Density % sol: 32.24 %
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: ID29 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 5, 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: 1.55→45.56 Å / Num. all: 44356 / Num. obs: 44187 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 13.8
Reflection shellResolution: 1.55→1.63 Å / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 3.3 / % 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 4ORR

4orr


Resolution: 1.55→45.565 Å / SU ML: 0.16 / σ(F): 1.34 / Phase error: 23.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2349 2227 5.04 %RANDOM
Rwork0.2082 ---
obs0.2096 44155 99.55 %-
all-44356 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.55→45.565 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2490 0 76 84 2650
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042627
X-RAY DIFFRACTIONf_angle_d0.8863522
X-RAY DIFFRACTIONf_dihedral_angle_d15.2821005
X-RAY DIFFRACTIONf_chiral_restr0.063370
X-RAY DIFFRACTIONf_plane_restr0.003444
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.58370.29441560.26842585X-RAY DIFFRACTION100
1.5837-1.62060.26091350.25452581X-RAY DIFFRACTION99
1.6206-1.66110.27321490.23642584X-RAY DIFFRACTION99
1.6611-1.7060.28461120.22592629X-RAY DIFFRACTION100
1.706-1.75620.23941370.2192645X-RAY DIFFRACTION100
1.7562-1.81290.25361230.21662580X-RAY DIFFRACTION100
1.8129-1.87770.26871380.21452613X-RAY DIFFRACTION100
1.8777-1.95290.2471460.21172621X-RAY DIFFRACTION99
1.9529-2.04170.27291310.20612597X-RAY DIFFRACTION99
2.0417-2.14940.21881320.2022610X-RAY DIFFRACTION100
2.1494-2.2840.19931370.21162637X-RAY DIFFRACTION100
2.284-2.46040.25011480.21832615X-RAY DIFFRACTION99
2.4604-2.7080.25991300.22482614X-RAY DIFFRACTION100
2.708-3.09970.25151560.22652645X-RAY DIFFRACTION100
3.0997-3.9050.2361310.19452650X-RAY DIFFRACTION99
3.905-45.58470.20241660.18742722X-RAY DIFFRACTION100
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)
11.779-0.1855-0.2392.05480.39261.8870.0140.03770.01470.1636-0.0515-0.27830.00190.07540.0370.0996-0.004-0.03810.12190.01070.104720.83481.56760.2488
23.6940.8687-1.06962.8094-0.30291.21620.21410.08780.0991-0.0713-0.1709-0.0928-0.0743-0.0689-0.02990.14980.01970.05740.21270.05440.187544.175-22.7149-13.8576
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 29:187 OR RESID 301:349 ) ) OR ( CHAIN B AND RESID 201:201 )A29 - 187
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 29:187 OR RESID 301:349 ) ) OR ( CHAIN B AND RESID 201:201 )A301 - 349
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 29:187 OR RESID 301:349 ) ) OR ( CHAIN B AND RESID 201:201 )B201
4X-RAY DIFFRACTION2( CHAIN B AND ( RESID 29:187 OR RESID 202:235 ) )B29 - 187
5X-RAY DIFFRACTION2( CHAIN B AND ( RESID 29:187 OR RESID 202:235 ) )B202 - 235

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