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

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Basic information

Entry
Database: PDB / ID: 4orw
TitleThree-dimensional structure of the C65A-K59A double 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 / 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: 1.664 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 / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 27, 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


Theoretical massNumber of molelcules
Total (without water)41,9192
Polymers41,9192
Non-polymers00
Water2,162120
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
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.330, 57.630, 131.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 1.73 Å3/Da / Density % sol: 28.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris, 2.0M Ammonium Sulphate, pH 8.5, 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: 1.66→57.63 Å / Num. all: 35158 / Num. obs: 34796 / % possible obs: 99.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 13
Reflection shellResolution: 1.66→1.75 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 3.7 / % possible all: 99.4

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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: 1.664→52.803 Å / SU ML: 0.2 / σ(F): 1.35 / Phase error: 22.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2398 1743 5.02 %RANDOM
Rwork0.2013 ---
obs0.2032 34739 98.81 %-
all-35158 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.664→52.803 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2482 0 0 120 2602
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042542
X-RAY DIFFRACTIONf_angle_d0.9033436
X-RAY DIFFRACTIONf_dihedral_angle_d12.586922
X-RAY DIFFRACTIONf_chiral_restr0.062370
X-RAY DIFFRACTIONf_plane_restr0.003442
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.664-1.7130.30191590.24432680X-RAY DIFFRACTION99
1.713-1.76830.28831210.23222732X-RAY DIFFRACTION99
1.7683-1.83150.25481490.20982728X-RAY DIFFRACTION99
1.8315-1.90480.26951480.20432657X-RAY DIFFRACTION97
1.9048-1.99150.22671430.19512732X-RAY DIFFRACTION99
1.9915-2.09650.25041540.18732726X-RAY DIFFRACTION100
2.0965-2.22780.23121400.1882740X-RAY DIFFRACTION99
2.2278-2.39980.24881480.20192726X-RAY DIFFRACTION98
2.3998-2.64130.26611410.20652745X-RAY DIFFRACTION100
2.6413-3.02350.22691480.21652767X-RAY DIFFRACTION98
3.0235-3.80920.25821530.19222832X-RAY DIFFRACTION100
3.8092-52.82950.19481390.19662931X-RAY DIFFRACTION98
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)
10.8923-0.5509-0.02371.3262-0.42590.68970.03410.1236-0.0742-0.089-0.0060.08790.0358-0.0454-0.00620.054-0.0058-0.01130.0702-0.01540.062-0.6234-2.956123.0688
21.30340.1074-0.05930.813-0.09931.75460.09670.17040.1386-0.1656-0.0035-0.14610.0080.1581-0.04730.09980.01520.03450.10570.0160.098111.6204-31.294812.1577
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 29:187 OR RESID 201:268 ) ) OR ( CHAIN B AND RESID 201:201 )A29 - 187
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 29:187 OR RESID 201:268 ) ) OR ( CHAIN B AND RESID 201:201 )A201 - 268
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 29:187 OR RESID 201:268 ) ) OR ( CHAIN B AND RESID 201:201 )B201
4X-RAY DIFFRACTION2( CHAIN A AND RESID 269:269 ) OR ( CHAIN B AND ( RESID 29:187 OR RESID 202:251 ) )A269
5X-RAY DIFFRACTION2( CHAIN A AND RESID 269:269 ) OR ( CHAIN B AND ( RESID 29:187 OR RESID 202:251 ) )B29 - 187
6X-RAY DIFFRACTION2( CHAIN A AND RESID 269:269 ) OR ( CHAIN B AND ( RESID 29:187 OR RESID 202:251 ) )B202 - 251

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