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

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Basic information

Entry
Database: PDB / ID: 4ors
TitleThree-dimensional structure of the C65A 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 / Transcriptional regulation of testis differentiation / prostaglandin-D synthase activity / negative regulation of male germ cell proliferation / regulation of circadian sleep/wake cycle, sleep / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / cyclooxygenase pathway / retinoid binding / prostaglandin biosynthetic process / mast cell degranulation ...prostaglandin-D synthase / Transcriptional regulation of testis differentiation / prostaglandin-D synthase activity / negative regulation of male germ cell proliferation / regulation of circadian sleep/wake cycle, sleep / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / cyclooxygenase pathway / retinoid binding / prostaglandin biosynthetic process / mast cell degranulation / rough endoplasmic reticulum / response to glucocorticoid / 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 / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding 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: 1.4 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 1.3Jan 29, 2020Group: Data collection / Database references / Category: reflns / struct_ref_seq_dif
Item: _reflns.pdbx_Rmerge_I_obs / _struct_ref_seq_dif.details
Revision 1.4Sep 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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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)42,1313
Polymers42,0352
Non-polymers961
Water3,495194
1
A: Prostaglandin-H2 D-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1142
Polymers21,0181
Non-polymers961
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 area1660 Å2
ΔGint-27 kcal/mol
Surface area17220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.127, 45.819, 49.151
Angle α, β, γ (deg.)73.12, 82.82, 64.90
Int Tables number1
Space group name H-MP1
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: 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-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O

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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 Å3/Da / Density % sol: 38.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Na Hepes, 2% PEG 400, 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: ID14-1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 22, 2007
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.4→40.03 Å / Num. all: 64247 / Num. obs: 60070 / % possible obs: 93.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.2 % / Rmerge(I) obs: 0.118 / Net I/σ(I): 8
Reflection shellResolution: 1.4→1.48 Å / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 2.1 / % possible all: 91.9

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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: 1.4→22.383 Å / SU ML: 0.2 / σ(F): 1.36 / Phase error: 27.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2799 3063 5.12 %RANDOM
Rwork0.2498 ---
obs0.2513 60070 86.06 %-
all-64247 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→22.383 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2545 0 5 194 2744
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052610
X-RAY DIFFRACTIONf_angle_d0.8713528
X-RAY DIFFRACTIONf_dihedral_angle_d14.314951
X-RAY DIFFRACTIONf_chiral_restr0.062381
X-RAY DIFFRACTIONf_plane_restr0.004453
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.41590.31851660.29723164X-RAY DIFFRACTION78
1.4159-1.43260.33681930.28793431X-RAY DIFFRACTION84
1.4326-1.450.29641990.28053452X-RAY DIFFRACTION85
1.45-1.46840.29091960.28453388X-RAY DIFFRACTION85
1.4684-1.48770.31361820.27683550X-RAY DIFFRACTION86
1.4877-1.50810.30071770.25933369X-RAY DIFFRACTION86
1.5081-1.52960.30561970.26493584X-RAY DIFFRACTION85
1.5296-1.55240.30621720.25453435X-RAY DIFFRACTION87
1.5524-1.57670.28481800.25643579X-RAY DIFFRACTION86
1.5767-1.60250.27761740.25173542X-RAY DIFFRACTION87
1.6025-1.63020.29431970.25243474X-RAY DIFFRACTION87
1.6302-1.65980.27662290.24663585X-RAY DIFFRACTION88
1.6598-1.69170.27861560.24963554X-RAY DIFFRACTION87
1.6917-1.72620.2762040.24723492X-RAY DIFFRACTION88
1.7262-1.76370.27611920.23973587X-RAY DIFFRACTION87
1.7637-1.80480.27172000.24623573X-RAY DIFFRACTION88
1.8048-1.84990.2462070.23893567X-RAY DIFFRACTION88
1.8499-1.89990.28851910.2363574X-RAY DIFFRACTION88
1.8999-1.95570.22661860.24123606X-RAY DIFFRACTION88
1.9557-2.01880.24381840.24273563X-RAY DIFFRACTION89
2.0188-2.09090.27042060.23433651X-RAY DIFFRACTION89
2.0909-2.17460.26541810.23273735X-RAY DIFFRACTION90
2.1746-2.27350.28271980.24913670X-RAY DIFFRACTION91
2.2735-2.39320.25122210.24183651X-RAY DIFFRACTION91
2.3932-2.54290.28012100.2413695X-RAY DIFFRACTION91
2.5429-2.7390.25932130.25123679X-RAY DIFFRACTION92
2.739-3.0140.28251930.25063714X-RAY DIFFRACTION91
3.014-3.44880.31451580.24443569X-RAY DIFFRACTION87
3.4488-4.33990.28391700.2462999X-RAY DIFFRACTION73
4.3399-22.38580.32231260.28542465X-RAY DIFFRACTION61
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)
11.0762-0.14790.03851.14950.17710.86140.0404-0.16450.06760.15730.0261-0.0694-0.04380.0316-0.03990.0764-0.00620.00350.0709-0.0110.0484-0.0111-0.04661.1244
21.1176-0.09240.48671.02170.06751.01390.04010.0665-0.0748-0.16050.00330.0467-0.0004-0.0286-0.0230.07040.0028-0.00320.07020.00150.0557-19.5366-5.094828.4964
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 27:188 OR RESID 201:201 OR RESID 301:392 ) ) OR ( CHAIN B AND RESID 201:201 )A27 - 188
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 27:188 OR RESID 201:201 OR RESID 301:392 ) ) OR ( CHAIN B AND RESID 201:201 )A201
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 27:188 OR RESID 201:201 OR RESID 301:392 ) ) OR ( CHAIN B AND RESID 201:201 )A301 - 392
4X-RAY DIFFRACTION1( CHAIN A AND ( RESID 27:188 OR RESID 201:201 OR RESID 301:392 ) ) OR ( CHAIN B AND RESID 201:201 )B201
5X-RAY DIFFRACTION2( CHAIN B AND ( RESID 27:189 OR RESID 202:302 ) )B27 - 189
6X-RAY DIFFRACTION2( CHAIN B AND ( RESID 27:189 OR RESID 202:302 ) )B202 - 302

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