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- PDB-3lu9: Crystal structure of human thrombin mutant S195A in complex with ... -

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Basic information

Entry
Database: PDB / ID: 3lu9
TitleCrystal structure of human thrombin mutant S195A in complex with the extracellular fragment of human PAR1
Components
  • (Prothrombin) x 2
  • Proteinase-activated receptor 1
KeywordsHYDROLASE / Serine protease / Acute phase / Blood coagulation / Calcium / Cleavage on pair of basic residues / Disease mutation / Disulfide bond / Gamma-carboxyglutamic acid / Glycoprotein / Kringle / Pharmaceutical / Polymorphism / Protease / Secreted / Zymogen / Cell membrane / G-protein coupled receptor / Membrane / Phosphoprotein / Receptor / Transducer / Transmembrane
Function / homology
Function and homology information


negative regulation of renin secretion into blood stream / negative regulation of glomerular filtration / dendritic cell homeostasis / establishment of synaptic specificity at neuromuscular junction / thrombin-activated receptor signaling pathway / thrombin-activated receptor activity / platelet dense tubular network / cell-cell junction maintenance / regulation of interleukin-1 beta production / platelet dense granule organization ...negative regulation of renin secretion into blood stream / negative regulation of glomerular filtration / dendritic cell homeostasis / establishment of synaptic specificity at neuromuscular junction / thrombin-activated receptor signaling pathway / thrombin-activated receptor activity / platelet dense tubular network / cell-cell junction maintenance / regulation of interleukin-1 beta production / platelet dense granule organization / connective tissue replacement involved in inflammatory response wound healing / trans-synaptic signaling by endocannabinoid, modulating synaptic transmission / regulation of sensory perception of pain / positive regulation of smooth muscle contraction / positive regulation of calcium ion transport / : / positive regulation of Rho protein signal transduction / positive regulation of lipid kinase activity / : / cytolysis by host of symbiont cells / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin / regulation of blood coagulation / neutrophil-mediated killing of gram-negative bacterium / ligand-gated ion channel signaling pathway / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / negative regulation of astrocyte differentiation / negative regulation of platelet activation / positive regulation of collagen biosynthetic process / G-protein alpha-subunit binding / negative regulation of cytokine production involved in inflammatory response / anatomical structure morphogenesis / positive regulation of blood coagulation / negative regulation of fibrinolysis / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / positive regulation of vasoconstriction / homeostasis of number of cells within a tissue / release of sequestered calcium ion into cytosol / fibrinolysis / regulation of cytosolic calcium ion concentration / Intrinsic Pathway of Fibrin Clot Formation / Peptide ligand-binding receptors / positive regulation of GTPase activity / positive regulation of release of sequestered calcium ion into cytosol / acute-phase response / Regulation of Complement cascade / positive regulation of interleukin-8 production / negative regulation of proteolysis / G protein-coupled receptor activity / Cell surface interactions at the vascular wall / lipopolysaccharide binding / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / neuromuscular junction / positive regulation of insulin secretion / caveola / regulation of synaptic plasticity / platelet activation / : / response to wounding / positive regulation of protein localization to nucleus / Golgi lumen / positive regulation of interleukin-6 production / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of reactive oxygen species metabolic process / blood coagulation / G-protein beta-subunit binding / antimicrobial humoral immune response mediated by antimicrobial peptide / late endosome / Thrombin signalling through proteinase activated receptors (PARs) / heparin binding / regulation of cell shape / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / positive regulation of cell growth / G alpha (q) signalling events / collagen-containing extracellular matrix / positive regulation of canonical NF-kappaB signal transduction / postsynaptic membrane / negative regulation of neuron apoptotic process / blood microparticle / response to lipopolysaccharide / positive regulation of MAPK cascade / positive regulation of ERK1 and ERK2 cascade / early endosome / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor signaling pathway / positive regulation of cell migration / inflammatory response / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / negative regulation of cell population proliferation / endoplasmic reticulum lumen / serine-type endopeptidase activity
Similarity search - Function
Thrombin receptor / Protease-activated receptor / Epsilon-Thrombin; Chain L / Thrombin light chain domain / Prothrombin/thrombin / Thrombin light chain / Thrombin light chain domain superfamily / : / Thrombin light chain / Kringle domain ...Thrombin receptor / Protease-activated receptor / Epsilon-Thrombin; Chain L / Thrombin light chain domain / Prothrombin/thrombin / Thrombin light chain / Thrombin light chain domain superfamily / : / Thrombin light chain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain superfamily / Vitamin K-dependent carboxylation domain. / Gla domain profile. / Domain containing Gla (gamma-carboxyglutamate) residues. / Kringle-like fold / G-protein coupled receptors family 1 signature. / Few Secondary Structures / Irregular / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Prothrombin / Proteinase-activated receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGandhi, P.S. / Chen, Z. / Di Cera, E.
Citation
Journal: J.Biol.Chem. / Year: 2010
Title: Crystal structure of thrombin bound to the uncleaved extracellular fragment of PAR1.
Authors: Gandhi, P.S. / Chen, Z. / Di Cera, E.
#1: Journal: J.Biol.Chem. / Year: 2004
Title: Molecular dissection of NA+ binding to thrombin
Authors: Pineda, A.O. / Carrell, C.J. / Bush, L.A. / Prasad, S. / Caccia, S. / Chen, Z. / Mathews, F.S. / Di Cera, E.
History
DepositionFeb 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_PDB_ins_code / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Oct 13, 2021Group: Advisory / Database references / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_unobs_or_zero_occ_residues / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Prothrombin
B: Prothrombin
C: Proteinase-activated receptor 1
D: Prothrombin
E: Prothrombin
F: Proteinase-activated receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,84111
Polymers76,2616
Non-polymers5805
Water12,574698
1
A: Prothrombin
B: Prothrombin
C: Proteinase-activated receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4676
Polymers38,1303
Non-polymers3363
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7020 Å2
ΔGint-33 kcal/mol
Surface area13770 Å2
MethodPISA
2
D: Prothrombin
E: Prothrombin
F: Proteinase-activated receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3755
Polymers38,1303
Non-polymers2442
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6440 Å2
ΔGint-32 kcal/mol
Surface area14350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.334, 50.171, 85.502
Angle α, β, γ (deg.)76.39, 83.93, 73.74
Int Tables number1
Space group name H-MP1

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Components

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Protein/peptide , 2 types, 4 molecules ADCF

#1: Protein/peptide Prothrombin / Coagulation factor II / Activation peptide fragment 1 / Activation peptide fragment 2 / Thrombin ...Coagulation factor II / Activation peptide fragment 1 / Activation peptide fragment 2 / Thrombin light chain / Thrombin heavy chain


Mass: 5367.890 Da / Num. of mol.: 2 / Mutation: S195A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F2, Human / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P00734, thrombin
#3: Protein/peptide Proteinase-activated receptor 1 / PAR-1 / Thrombin receptor / Coagulation factor II receptor


Mass: 2998.284 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F2R, CF2R, PAR1, TR / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P25116

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Protein / Sugars , 2 types, 4 molecules BE

#2: Protein Prothrombin / Coagulation factor II / Activation peptide fragment 1 / Activation peptide fragment 2 / Thrombin ...Coagulation factor II / Activation peptide fragment 1 / Activation peptide fragment 2 / Thrombin light chain / Thrombin heavy chain


Mass: 29764.219 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F2 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P00734, thrombin
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 701 molecules

#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 698 / 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: 2.43 Å3/Da / Density % sol: 49.37 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 200mM K/Na tartrate, 20% PEG3350, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 31, 2009
RadiationMonochromator: Bent Ge(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. all: 65636 / Num. obs: 63011 / % possible obs: 96 % / Observed criterion σ(F): -1.2 / Observed criterion σ(I): -1.2 / Redundancy: 3.1 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 17.6
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 3.9 / Num. unique all: 3066 / % possible all: 93.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPfrom CCP4phasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SHH

1shh


Resolution: 1.8→28.07 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.919 / SU B: 6.991 / SU ML: 0.099 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): -1.2 / σ(I): -1.2 / ESU R: 0.144 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23622 3162 5 %RANDOM
Rwork0.19301 ---
obs0.19513 60703 96 %-
all-63232 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.354 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20.03 Å2-0.12 Å2
2---0.1 Å20.06 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.8→28.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5215 0 36 698 5949
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225388
X-RAY DIFFRACTIONr_angle_refined_deg1.4951.9657279
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9195631
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.32923.333264
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.64415933
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8661546
X-RAY DIFFRACTIONr_chiral_restr0.1190.2752
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214128
X-RAY DIFFRACTIONr_mcbond_it0.7531.53188
X-RAY DIFFRACTIONr_mcangle_it1.35325137
X-RAY DIFFRACTIONr_scbond_it2.11532200
X-RAY DIFFRACTIONr_scangle_it3.3314.52142
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 213 -
Rwork0.241 4400 -
obs--93.44 %
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)
10.96230.78690.20784.18270.32685.1874-0.31070.40720.2425-1.0680.340.2550.7135-0.1611-0.02940.4904-0.1457-0.06420.26280.06310.15512.15288.5286-14.4363
21.8518-0.63120.216211.0094-3.58042.7609-0.0294-0.04730.19630.59990.11760.1781-0.47010.0601-0.08820.08460.00050.01420.0512-0.04150.10055.207118.51264.9601
31.4020.91670.0923.55870.54660.5981-0.1185-0.02360.289-0.23210.27980.7014-0.012-0.14-0.16130.046-0.0076-0.06450.14360.12210.2936-7.75553.1770.5465
41.03660.8026-0.4093.8556-1.11111.0691-0.19630.14430.1091-0.76170.35790.48680.3169-0.1692-0.16160.166-0.0712-0.10370.07410.0310.0988-4.5264-1.7969-3.9119
50.89780.3717-0.01544.3115-1.23271.51380.0106-0.0796-0.10650.19930.01110.00460.1332-0.0541-0.02170.04660.0097-0.00010.0563-0.00460.07043.3512-5.166910.9017
60.97380.6752-0.1393.8643-1.18291.743-0.11910.0683-0.0818-0.56840.113-0.1490.41720.02120.00620.13110.0020.01820.0451-0.0230.06954.7218-4.85480.1493
718.1288-2.556810.94368.18210.604312.58650.2837-0.5074-1.28590.38810.3198-1.23360.5031-0.1291-0.60350.04520.0493-0.02230.28310.16970.7808-21.33632.41765.0357
81.10630.8161-0.2174.39410.894710.02870.0621-0.24580.4065-0.1247-0.02780.0703-1.007-0.4069-0.03430.17220.08220.04510.1443-0.07960.199516.925340.766742.6617
92.97754.11512.538.93794.05829.84580.0333-0.03560.7014-0.5773-0.43020.9534-1.3539-1.490.39690.33390.33010.02090.393-0.05030.24428.506236.655330.4829
101.61490.39980.41812.87691.79145.61260.2004-0.0617-0.07460.42470.4492-0.54240.99211.2789-0.64960.20320.2426-0.1270.3581-0.15380.142731.184722.770239.4769
111.33560.4350.33482.40832.37776.56980.1918-0.0743-0.02060.6085-0.0051-0.14711.2086-0.0825-0.18670.25740.0062-0.04150.079-0.00640.028119.243121.124839.6368
1218.52691.1013-3.605416.226323.551335.6705-1.5015-0.1745-1.40172.8491.5518-0.51354.68952.0255-0.05031.40370.32680.33281.0476-0.17620.826333.585819.42219.204
131.36630.37160.70572.75363.50247.59030.17730.01650.03030.3-0.30920.14420.8254-0.75780.1320.12-0.04710.01180.1471-0.01430.032513.766722.171830.2672
141.68710.17250.20451.83622.574310.32110.1384-0.0015-0.19890.6781-0.1018-0.07122.3692-0.3921-0.03650.6066-0.069-0.03080.0238-0.00590.050117.028914.183935.7901
1516.518-0.5679.13269.41530.050531.6370.92160.8618-2.1834-0.72750.37550.75452.7549-1.7951-1.29720.3386-0.1215-0.12020.88-0.14830.660240.923225.011232.725
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 8
2X-RAY DIFFRACTION2A9 - 14
3X-RAY DIFFRACTION3B16 - 52
4X-RAY DIFFRACTION4B53 - 140
5X-RAY DIFFRACTION5B141 - 199
6X-RAY DIFFRACTION6B200 - 361
7X-RAY DIFFRACTION7B362 - 375
8X-RAY DIFFRACTION8D1 - 11
9X-RAY DIFFRACTION9D12 - 14
10X-RAY DIFFRACTION10E16 - 90
11X-RAY DIFFRACTION11E91 - 146
12X-RAY DIFFRACTION12E147 - 152
13X-RAY DIFFRACTION13E153 - 216
14X-RAY DIFFRACTION14E217 - 359
15X-RAY DIFFRACTION15E360 - 375

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