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- PDB-7rof: Engineered tryptophan synthase b-subunit from Pyrococcus furiosus... -

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Basic information

Entry
Database: PDB / ID: 7rof
TitleEngineered tryptophan synthase b-subunit from Pyrococcus furiosus, PfTrpB2B9-H275E with L-Trp non-covalently bound
ComponentsTryptophan synthase beta chain 1
KeywordsBIOSYNTHETIC PROTEIN / tryptophan synthase
Function / homology
Function and homology information


tryptophan synthase / tryptophan synthase activity / cytoplasm
Similarity search - Function
Tryptophan synthase, beta chain, conserved site / Tryptophan synthase, beta chain / Tryptophan synthase beta chain/beta chain-like / Tryptophan synthase beta chain pyridoxal-phosphate attachment site. / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate dependent enzyme
Similarity search - Domain/homology
TRYPTOPHAN / Tryptophan synthase beta chain 1
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsHiggins, P.M. / Buller, A.R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)DP2-GM137417 United States
National Science Foundation (NSF, United States)DGE-1747503 United States
CitationJournal: Nat Commun / Year: 2022
Title: Substrate multiplexed protein engineering facilitates promiscuous biocatalytic synthesis.
Authors: McDonald, A.D. / Higgins, P.M. / Buller, A.R.
History
DepositionJul 30, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tryptophan synthase beta chain 1
B: Tryptophan synthase beta chain 1
C: Tryptophan synthase beta chain 1
D: Tryptophan synthase beta chain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,93910
Polymers174,4394
Non-polymers5006
Water1629
1
A: Tryptophan synthase beta chain 1
B: Tryptophan synthase beta chain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,4705
Polymers87,2192
Non-polymers2503
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-40 kcal/mol
Surface area25410 Å2
MethodPISA
2
C: Tryptophan synthase beta chain 1
D: Tryptophan synthase beta chain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,4705
Polymers87,2192
Non-polymers2503
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-38 kcal/mol
Surface area25240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.402, 82.658, 322.255
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Tryptophan synthase beta chain 1


Mass: 43609.688 Da / Num. of mol.: 4 / Mutation: H275E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: trpB1, PF1706 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8U093, tryptophan synthase
#2: Chemical ChemComp-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C11H12N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 45.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.85 / Details: 13-21% PEG3350, 0.1 M HEPES pH 7.85

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.033167 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 28, 2021
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033167 Å / Relative weight: 1
ReflectionResolution: 2.39→50 Å / Num. obs: 823988 / % possible obs: 99.5 % / Redundancy: 13.4 % / CC1/2: 0.998 / Rpim(I) all: 0.058 / Net I/σ(I): 8.4
Reflection shellResolution: 2.39→2.45 Å / Redundancy: 14.1 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 62539 / CC1/2: 0.488 / Rpim(I) all: 1.548 / % possible all: 99.5
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6AM8
Resolution: 2.39→46.695 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.935 / SU B: 34.382 / SU ML: 0.326 / Cross valid method: FREE R-VALUE / ESU R: 0.496 / ESU R Free: 0.289
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2714 3098 5.031 %
Rwork0.2272 58486 -
all0.229 --
obs-61584 99.305 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 72.415 Å2
Baniso -1Baniso -2Baniso -3
1-1.735 Å20 Å20 Å2
2--5.909 Å2-0 Å2
3----7.644 Å2
Refinement stepCycle: LAST / Resolution: 2.39→46.695 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11078 0 34 9 11121
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01311381
X-RAY DIFFRACTIONr_bond_other_d0.0010.01710524
X-RAY DIFFRACTIONr_angle_refined_deg1.2151.63215524
X-RAY DIFFRACTIONr_angle_other_deg1.1651.57323958
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.82251539
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.1821.904457
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.577151580
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6241551
X-RAY DIFFRACTIONr_chiral_restr0.040.21512
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213270
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022548
X-RAY DIFFRACTIONr_nbd_refined0.1760.22162
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1730.29767
X-RAY DIFFRACTIONr_nbtor_refined0.1520.25578
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.25000
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2224
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2050.28
X-RAY DIFFRACTIONr_nbd_other0.2030.240
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2160.21
X-RAY DIFFRACTIONr_mcbond_it0.7463.0166153
X-RAY DIFFRACTIONr_mcbond_other0.7463.0166152
X-RAY DIFFRACTIONr_mcangle_it1.2934.5227681
X-RAY DIFFRACTIONr_mcangle_other1.2934.5227682
X-RAY DIFFRACTIONr_scbond_it0.693.0445228
X-RAY DIFFRACTIONr_scbond_other0.693.0445228
X-RAY DIFFRACTIONr_scangle_it1.1894.5447839
X-RAY DIFFRACTIONr_scangle_other1.1894.5447839
X-RAY DIFFRACTIONr_lrange_it2.91335.81212105
X-RAY DIFFRACTIONr_lrange_other2.91335.81112106
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.39-2.4520.3972090.3944232X-RAY DIFFRACTION99.3512
2.452-2.5190.392150.3784162X-RAY DIFFRACTION99.2067
2.519-2.5920.3592140.3464016X-RAY DIFFRACTION99.3424
2.592-2.6710.3691900.3273924X-RAY DIFFRACTION99.396
2.671-2.7590.2912070.2823805X-RAY DIFFRACTION99.4793
2.759-2.8550.2991900.2733722X-RAY DIFFRACTION99.5673
2.855-2.9630.3211860.2663578X-RAY DIFFRACTION99.6031
2.963-3.0830.291820.2493343X-RAY DIFFRACTION96.9739
3.083-3.220.2731860.2243303X-RAY DIFFRACTION99.7712
3.22-3.3760.2671800.2063174X-RAY DIFFRACTION99.6435
3.376-3.5580.2571450.2023036X-RAY DIFFRACTION99.8117
3.558-3.7720.2451560.1982849X-RAY DIFFRACTION99.4046
3.772-4.0310.2761340.1792730X-RAY DIFFRACTION99.7909
4.031-4.3520.2531370.1842543X-RAY DIFFRACTION99.9254
4.352-4.7640.2351330.1742342X-RAY DIFFRACTION99.8386
4.764-5.320.2311120.1772134X-RAY DIFFRACTION100
5.32-6.1310.3011130.2381819X-RAY DIFFRACTION96.2151
6.131-7.4810.281860.2341650X-RAY DIFFRACTION100
7.481-10.4640.228710.2061300X-RAY DIFFRACTION99.8543
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.1245-0.9808-1.37991.83630.1633.18190.05520.1112-0.191-0.1008-0.0851-0.06430.26880.31860.02990.37330.0395-0.05860.0569-0.02270.406710.9871-7.0577-79.0051
26.1827-1.6174-2.79149.75742.92999.84620.0487-0.0554-0.0574-0.3439-0.0332-0.0781-0.06990.8239-0.01550.2830.0088-0.04330.3880.01260.464725.2496-5.4182-77.9977
31.77530.392-1.11023.5035-3.08347.14340.1196-0.3130.4281-0.01190.1312-0.4212-0.76310.5275-0.25080.405-0.06940.02210.508-0.06570.721328.2855.8869-74.8875
46.2115-1.6989-2.00551.48890.54483.56620.1513-0.0692-0.0543-0.1779-0.1318-0.3294-0.10990.9167-0.01950.40130.0677-0.0230.3152-0.01210.372416.7337-5.7477-84.3759
52.47850.40760.02684.2092-0.43562.65210.05510.166-0.1438-0.3107-0.04940.0455-0.0026-0.1053-0.00570.34260.0889-0.03650.0376-0.00140.33710.20952.4343-83.3356
66.1387-0.6788-0.12898.15132.06884.28140.064-0.03060.8866-0.81470.0817-0.2307-0.62730.0775-0.14570.5750.03560.02470.44920.07420.481112.046710.9872-96.0911
73.10542.35562.26327.15054.42924.7776-0.03510.36140.1512-0.0689-0.0113-0.42380.0530.46780.04640.45310.06380.02420.17040.06440.429910.52568.7098-86.0684
82.31510.86142.78846.47522.65974.7147-0.14270.33570.2621-0.4962-0.01010.4651-0.6456-0.10990.15280.3540.13840.05460.32240.09590.39540.00788.5534-83.3644
93.6325-1.3461-1.77462.8649-1.75556.30990.3328-0.14290.27260.0067-0.17140.2903-0.30240.0272-0.16140.3211-0.00470.0030.0549-0.05990.421-2.33396.1586-72.3427
104.47020.8581-0.86261.3242-1.03426.4425-0.1069-0.28590.21840.05940.13340.19140.10420.3031-0.02650.4894-0.0024-0.03180.40270.03660.572712.411213.7837-68.8499
111.9818-0.6595-0.84442.23911.16654.9378-0.0152-0.5755-0.07050.5980.05640.05510.34710.0236-0.04120.6047-0.0061-0.02550.190.06530.4244.3652-5.8214-48.608
127.25570.97831.49386.0318-0.75466.53350.124-0.97830.48060.5105-0.4037-0.5921-0.84090.95820.27970.6744-0.05630.03560.3957-0.04020.43326.44911.2896-52.3189
130.0682-0.3242-0.28134.15363.91773.8167-0.1847-0.14030.0021-0.3480.1069-0.0673-0.63590.26710.07781.39910.1239-0.1111.1937-0.04370.74165.076615.1268-39.9332
143.0436-1.3155-0.40212.78970.04922.8622-0.039-0.427-0.16160.4348-0.0061-0.07130.39190.2690.04510.7420.06-0.03150.31290.09580.39897.9642-9.9731-45.6505
158.09063.38750.91597.52152.2182.92020.0874-0.8122-0.07870.1735-0.32080.44970.2420.43610.23340.78580.1377-0.10290.60820.10160.375319.6564-13.5535-42.6401
167.46161.5685-1.00843.3212.49322.65350.31340.0312-0.28880.1259-0.005-0.4903-0.17040.2016-0.30841.0527-0.0247-0.15951.0610.07390.459719.9025-1.4744-31.7709
170.869-0.28890.93810.43080.84196.0840.0542-0.20150.12590.11320.0336-0.1647-0.20480.1061-0.08780.7452-0.0554-0.01610.6766-0.01860.642922.49294.3691-36.9907
182.4047-1.4093-0.42172.01032.62635.9185-0.1058-0.5374-0.3130.48260.3358-0.10610.21921.0698-0.231.1981-0.1283-0.38231.10770.23410.488919.7955-9.4941-37.9954
192.06370.5199-1.73180.3972-1.16713.69450.0143-0.6412-0.2553-0.0285-0.2188-0.16530.39570.96830.20450.76720.2603-0.28560.6822-0.07940.625724.8774-10.1444-54.7326
2013.60131.8219-0.27448.21110.26132.05490.00290.26720.835-0.0855-0.00470.0869-0.24830.28250.00170.6175-0.0185-0.03380.5988-0.05040.585224.90116.4539-57.0377
210.27561.10060.06266.099-0.27340.26220.1732-0.19390.0761.1277-0.3457-0.4278-0.21310.06630.17261.371-0.2132-0.03411.1565-0.22650.5694-13.5912-28.634814.8978
224.61882.43790.61023.76790.93433.13960.1315-0.25670.09560.3276-0.18350.0548-0.2307-0.08250.0520.63090.02320.0270.3191-0.03690.3862-21.3601-32.2212-8.6093
236.93110.71451.53113.91050.262510.4889-0.1066-0.5006-0.47060.67150.0783-0.26050.4975-0.14980.02830.7237-0.0944-0.04680.6165-0.07220.4738-5.2642-33.2355-4.3977
242.15780.8534-3.23240.3585-1.42176.9110.0952-0.2422-0.75480.0929-0.068-0.21070.47980.2952-0.02721.09550.0145-0.2890.85210.01920.935-0.272-42.655-5.7686
251.8057-2.8751-3.46294.84735.79266.95270.31630.0619-0.1391-0.2586-0.53840.0412-0.3067-0.58050.2220.9877-0.0363-0.15580.94050.09921.1046-1.0802-43.12067.6903
268.40086.22060.05316.09382.21293.27460.1106-0.6587-0.2870.3298-0.169-0.28650.13980.56680.05841.0268-0.1929-0.16170.63790.08230.4489-9.815-30.5877.0768
271.67310.9011-0.27113.7956-1.04287.41550.2255-0.20910.16880.6441-0.27390.4558-0.3678-0.6920.04840.6883-0.01830.11360.3947-0.12120.4487-31.3009-37.0034-1.4312
280.4268-1.14330.83284.136-0.31848.1067-0.0573-0.1026-0.14920.68660.00490.08980.82770.73970.05241.2987-0.0589-0.02751.01960.25290.7143-17.3191-50.528611.3389
292.58210.2858-0.59472.36230.9226.46380.0862-0.1884-0.30370.3576-0.15050.30040.5355-0.56070.06430.7731-0.03950.10650.33220.03550.4844-28.4109-48.2106-2.5988
308.2264-0.4539-0.50146.1349-0.76791.7404-0.0606-0.0399-0.1206-0.02170.2434-0.29720.31630.1583-0.18280.68210.0196-0.01440.5272-0.0120.5999-13.7313-55.1158-11.4317
311.11450.1907-0.22392.14240.58434.8251-0.21260.3763-0.0584-0.05470.17580.2101-0.1251-0.16310.03680.4633-0.0174-0.01440.33920.00320.4371-22.5563-37.4219-33.0416
325.5812-1.61550.9744.0645-0.50347.514-0.02640.5155-0.18950.03180.0338-0.00180.66650.1151-0.00740.661-0.07280.05980.2448-0.06960.4917-21.7915-53.808-29.9947
333.00880.053-2.75410.65871.5166.4137-0.11880.3934-0.0501-0.00520.1678-0.1090.08390.2833-0.04890.6336-0.00040.0370.58120.01510.6316-14.8533-58.5179-32.4323
342.56231.67330.61132.71190.56494.2176-0.22190.3898-0.071-0.03060.13570.20290.0278-0.07150.08630.4816-0.0686-0.00960.33110.00560.3845-22.9331-39.3061-37.2751
356.23462.74581.22242.579-0.83483.9923-0.14610.5264-0.0091-0.05490.10190.2899-0.51270.67820.04420.5526-0.17430.00260.53790.0060.3196-12.1714-29.7578-37.5824
369.8399-5.6593.37793.3257-1.77232.2034-0.31870.30250.62810.12680.0593-0.51720.06521.080.25940.77110.02330.19461.1679-0.21750.6794-5.1348-42.4493-47.3457
370.9165-0.949-4.35351.67754.52620.886-0.14260.03030.0020.02550.0197-0.18720.55790.15750.12290.6290.0736-0.00510.7308-0.09380.7217-1.1171-48.0467-42.3765
385.85930.12910.80334.17642.19527.2363-0.14790.5103-0.0197-0.14870.2663-0.3062-0.07870.9851-0.11840.4801-0.15130.08550.675-0.04630.3918-7.8244-34.7412-42.3853
395.13120.73651.0060.13280.06624.5855-0.12680.37280.0587-0.00370.0555-0.1145-0.6881.10050.07140.6689-0.1435-0.01240.6214-0.05790.5824-4.7385-29.7822-25.8247
408.33410.98156.36323.9254-0.16555.28731.40270.7046-0.09680.1772-0.902-0.25731.13140.9239-0.50060.88240.2067-0.11640.8259-0.21091.1477-3.2234-45.8181-23.005
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA1 - 91
2X-RAY DIFFRACTION2ALLA92 - 119
3X-RAY DIFFRACTION3ALLA120 - 164
4X-RAY DIFFRACTION4ALLA165 - 213
5X-RAY DIFFRACTION5ALLA214 - 265
6X-RAY DIFFRACTION6ALLA266 - 290
7X-RAY DIFFRACTION7ALLA291 - 310
8X-RAY DIFFRACTION8ALLA311 - 333
9X-RAY DIFFRACTION9ALLA334 - 373
10X-RAY DIFFRACTION10ALLA374 - 401
11X-RAY DIFFRACTION11ALLB1 - 103
12X-RAY DIFFRACTION12ALLB104 - 148
13X-RAY DIFFRACTION13ALLB149 - 175
14X-RAY DIFFRACTION14ALLB176 - 238
15X-RAY DIFFRACTION15ALLB239 - 256
16X-RAY DIFFRACTION16ALLB257 - 281
17X-RAY DIFFRACTION17ALLB282 - 301
18X-RAY DIFFRACTION18ALLB302 - 327
19X-RAY DIFFRACTION19ALLB328 - 373
20X-RAY DIFFRACTION20ALLB374 - 385
21X-RAY DIFFRACTION21ALLC1 - 27
22X-RAY DIFFRACTION22ALLC28 - 99
23X-RAY DIFFRACTION23ALLC100 - 126
24X-RAY DIFFRACTION24ALLC127 - 152
25X-RAY DIFFRACTION25ALLC153 - 170
26X-RAY DIFFRACTION26ALLC171 - 197
27X-RAY DIFFRACTION27ALLC198 - 254
28X-RAY DIFFRACTION28ALLC255 - 301
29X-RAY DIFFRACTION29ALLC302 - 373
30X-RAY DIFFRACTION30ALLC374 - 385
31X-RAY DIFFRACTION31ALLD1 - 93
32X-RAY DIFFRACTION32ALLD94 - 142
33X-RAY DIFFRACTION33ALLD143 - 167
34X-RAY DIFFRACTION34ALLD168 - 219
35X-RAY DIFFRACTION35ALLD220 - 256
36X-RAY DIFFRACTION36ALLD257 - 282
37X-RAY DIFFRACTION37ALLD283 - 298
38X-RAY DIFFRACTION38ALLD299 - 327
39X-RAY DIFFRACTION39ALLD328 - 374
40X-RAY DIFFRACTION40ALLD375 - 401

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