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- PDB-4ld5: Crystal structure of MepR Q18P mutant from multidrug resistant S.... -

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Basic information

Entry
Database: PDB / ID: 4ld5
TitleCrystal structure of MepR Q18P mutant from multidrug resistant S. aureus clinical isolate
ComponentsMepR
KeywordsTRANSCRIPTION / multidrug resistance / winged helix-turn-helix / transcription repression
Function / homology
Function and homology information


response to stress / DNA-binding transcription factor activity
Similarity search - Function
MarR family / : / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
MarR family regulatory protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBirukou, I. / Brennan, R.G.
CitationJournal: MBio / Year: 2013
Title: The molecular mechanisms of allosteric mutations impairing MepR repressor function in multidrug-resistant strains of Staphylococcus aureus.
Authors: Birukou, I. / Tonthat, N.K. / Seo, S.M. / Schindler, B.D. / Kaatz, G.W. / Brennan, R.G.
History
DepositionJun 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MepR
E: MepR
F: MepR
H: MepR
D: MepR
C: MepR
B: MepR
G: MepR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,59415
Polymers135,9218
Non-polymers6727
Water3,891216
1
A: MepR
B: MepR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0763
Polymers33,9802
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4630 Å2
ΔGint-57 kcal/mol
Surface area13870 Å2
MethodPISA
2
E: MepR
F: MepR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1724
Polymers33,9802
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-70 kcal/mol
Surface area14970 Å2
MethodPISA
3
H: MepR
G: MepR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3656
Polymers33,9802
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5690 Å2
ΔGint-85 kcal/mol
Surface area14540 Å2
MethodPISA
4
D: MepR
C: MepR


Theoretical massNumber of molelcules
Total (without water)33,9802
Polymers33,9802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-52 kcal/mol
Surface area14840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.842, 45.841, 210.060
Angle α, β, γ (deg.)90.000, 97.300, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
MepR / MarR family transcription repressor MepR


Mass: 16990.170 Da / Num. of mol.: 8 / Mutation: Q18P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: mepR / Production host: Escherichia coli (E. coli) / References: UniProt: Q5Y812
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.59 Å3/Da / Density % sol: 52.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 0.2 M Na2SO4, 20% PEG 3350, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: May 20, 2013
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→42 Å / Num. all: 55487 / Num. obs: 51325 / % possible obs: 92.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1.7

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
CrystalCleardata collection
CrystalCleardata reduction
CrystalCleardata scaling
PHENIX(Phaser)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→34.929 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.38 / σ(F): 1.34 / Phase error: 30.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2684 1996 3.89 %random
Rwork0.211 ---
obs0.2132 51304 92.47 %-
all-55480 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 201.78 Å2 / Biso mean: 63.6185 Å2 / Biso min: 12.78 Å2
Refinement stepCycle: LAST / Resolution: 2.4→34.929 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8303 0 35 216 8554
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0128446
X-RAY DIFFRACTIONf_angle_d1.59511432
X-RAY DIFFRACTIONf_chiral_restr0.1121342
X-RAY DIFFRACTIONf_plane_restr0.0091469
X-RAY DIFFRACTIONf_dihedral_angle_d22.2673012
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.46010.36091410.31043486362793
2.4601-2.52660.34121510.30323489364093
2.5266-2.60090.3521290.29463474360392
2.6009-2.68480.36211500.27533512366293
2.6848-2.78070.30831310.26613488361993
2.7807-2.8920.31361470.25793515366292
2.892-3.02360.33721420.27033539368194
3.0236-3.18290.30871430.25223495363892
3.1829-3.38220.27231320.22773423355591
3.3822-3.6430.26241430.21743387353089
3.643-4.00920.30161360.1863366350288
4.0092-4.58820.23761470.16853453360089
4.5882-5.77640.21191490.19213761391097
5.7764-34.9290.25771550.2013920407598
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)
11.4925-0.36350.39472.2286-1.70053.71950.23090.2406-0.06-0.217-0.7464-0.30440.27131.60130.19190.54510.0301-0.04961.3660.22770.6331-6.065232.8968-95.4811
26.7217-0.20690.89693.4681-0.53194.41010.30040.35180.467-0.5843-0.1855-0.00110.8726-0.3961-0.15780.6641-0.0056-0.04740.7016-0.05170.2586-20.92130.9917-85.3807
35.36941.4051.84912.89610.23652.8608-0.11280.1502-0.5094-0.7801-0.2786-0.16562.67020.5467-0.03631.0089-0.00570.08950.7019-0.20360.5079-23.529120.8749-86.0037
44.13690.6184-0.14773.0625-0.02441.91130.22940.67250.3544-0.6390.14860.51860.22160.2392-0.30940.6069-0.0172-0.14650.65910.03680.342-33.266626.1412-80.859
57.77211.50621.56274.7310.12424.1072-0.25840.8058-0.7169-0.2431-0.138-0.1108-0.15390.6474-0.08450.423-0.0335-0.04370.6133-0.03790.31-21.080133.9011-79.2976
62.7917-0.97552.51751.3334-0.52454.69370.347-0.16570.65210.4-1.7171-0.30890.42070.8031.12760.6319-0.2245-0.02271.28330.38440.8636-0.954643.2652-88.3684
71.1636-1.60951.18625.6708-1.0477.24470.1202-0.35522.06481.2207-1.44581.0380.42250.421.18370.6975-0.11150.0390.7365-0.06390.7569-14.430645.6177-94.9773
82.3304-0.53860.60132.4907-0.97380.6692-0.62230.8876-0.0507-0.9891-0.0536-0.32830.6723-0.52070.050.7557-0.30110.17870.75360.00590.495923.859939.4491-60.0206
91.642-0.2991.05334.5866-0.16115.12780.32540.27520.1477-0.2115-0.15030.5058-0.09240.4431-0.18560.3247-0.02390.03860.51050.010.451216.093328.7358-41.7877
108.14762.9358-0.24639.56883.99985.79340.76720.6677-0.8105-0.5592-0.1518-0.86980.0361-0.0141-0.40970.56580.10780.04170.61980.00840.385923.772421.4722-41.8223
112.7230.4384-1.80611.6688-1.03373.7917-0.33530.60250.213-0.50490.5627-0.04040.2147-0.4174-0.1090.4887-0.15070.03640.590.03070.414514.803130.5569-45.6027
121.73431.822-0.90912.0455-0.52251.53870.0002-1.2774-0.70360.7026-0.1232-0.11060.58220.29670.02050.6767-0.11290.11970.94010.11290.573424.836730.5694-60.0006
131.6758-1.00412.28122.5695-2.37423.5772-0.1705-0.2792-0.10550.60460.45720.3521-0.4973-0.1128-0.33050.54820.08060.20870.7098-0.03620.693232.276241.3315-74.5167
141.7526-2.40730.17456.0767-2.6391.8863-0.1314-0.5730.7593-0.15460.3797-0.446-0.7534-0.2025-0.09250.7571-0.04830.07490.7644-0.16610.72236.937350.7052-76.4839
156.3542.2862-1.35670.7762-0.46810.27960.01740.90520.9488-0.04970.39390.63921.4277-1.1278-0.26160.7581-0.2979-0.03420.7867-0.01170.423627.013629.2973-75.7644
164.26631.85630.51128.28562.62393.92340.1110.59810.5847-1.5357-0.90380.67210.5476-0.23320.39651.0692-0.3148-0.15261.48830.40990.69712.304737.5202-69.7094
174.0807-0.85381.95882.4744-1.28612.682-0.49491.44340.2552-0.81360.21150.0681-0.50230.53890.17860.42180.0178-0.05690.54170.00560.3808-16.482323.4411-47.9164
182.08863.01620.27934.6935-1.24021.8278-0.38410.82960.0855-0.69840.1122-0.0476-0.04430.20110.2340.43770.0998-0.07570.29010.00590.2379-10.513316.8286-34.3714
195.4563-2.3828-1.09958.57621.91152.60020.39611.035-0.4264-0.3048-0.69540.05050.0346-0.3662-0.00830.56610.1379-0.0640.3069-0.01730.3541-14.97076.5442-33.6916
205.75483.32394.64337.58925.10956.86630.25491.1315-0.58460.27930.646-1.05750.92931.2052-0.29660.45450.188-0.01830.394-0.03580.2479-2.10838.2714-32.4815
211.3491.52650.90675.3565-1.04852.3778-0.21710.546-0.05170.15720.50690.44240.31630.1234-0.10360.26380.0390.03490.183-0.02030.4404-10.2023.0794-23.8732
223.3582-0.98092.44860.6412-0.96112.6254-0.11530.19820.28330.10190.06460.4024-0.1921-0.49880.06970.24980.0261-0.02220.35840.06370.3356-23.512821.0154-36.1944
233.71180.78560.72140.92591.75413.8447-0.1584-0.05070.2593-0.978-0.53220.318-1.44910.16620.50560.50040.1163-0.12070.28120.04350.342812.436119.1069-10.0375
240.0380.8091-0.02879.1366-1.8948.81290.66780.51960.0951-0.7064-0.31230.1631-0.2598-0.2834-0.2050.41030.0715-0.01730.3740.04980.30116.198431.21457.933
252.9422-1.15310.08154.87761.0655.19290.37530.65180.6502-0.9303-0.1453-0.4551-0.52120.4982-0.14810.4328-0.00080.05680.3810.1440.432723.657936.794310.5155
264.9926-1.6178-1.6972.96710.64993.4615-0.24250.1404-0.52120.44190.03750.12730.53330.13890.13740.72430.15640.07820.34070.13830.456812.583913.72663.412
271.0472-1.361.16071.7734-2.04367.6380.1423-0.01610.1852-0.0168-0.4482-0.3121-0.06121.36030.19920.30610.01930.0750.37260.01310.413214.837224.4193-10.3976
284.04552.1216-0.78016.04672.68125.99890.476-0.36980.86980.9222-0.48930.8848-0.0902-0.0162-0.05410.44850.07510.02670.2817-0.12480.3932-0.607630.1279-14.8133
298.70012.3844-0.33230.6733-0.25917.22310.8131-0.77380.7304-0.8547-0.29490.1436-1.2699-0.29570.17260.52230.02480.01990.1291-0.0290.52365.262336.8586-23.6692
305.6043-2.3961.39154.0443-0.54872.5482-0.0794-0.0348-0.1101-0.00230.05420.2871-0.17630.1510.07110.29410.0274-0.05580.18950.00380.20220.024626.3382-24.7569
314.0398-2.35293.50926.5314-0.36713.7170.3405-0.1120.2336-0.5930.2079-0.68-0.13131.07131.36240.3890.38140.00520.94130.19050.427324.572713.2576-11.8456
323.1568-3.4952-1.52793.87291.23378.5342-0.27120.472-0.94190.0115-0.0740.28991.50450.17370.27690.5643-0.03180.01590.2609-0.01330.446710.834810.0248-7.4825
332.2401-1.7308-0.10525.1363.93374.42930.015-0.3405-0.01960.1396-0.6140.1167-0.08850.51340.2530.521-0.05180.06310.79380.07160.4398-13.260332.9707-99.6527
348.07111.94731.41788.9193.3345.64790.6277-0.27931.2005-0.85610.0725-0.0342-1.1432-0.9757-0.16020.6592-0.1127-0.00930.87480.0180.551-3.960825.876-108.9956
352.6470.024-2.53114.9092-0.66022.5418-0.26890.9850.8835-0.4884-0.9867-1.99091.33960.9031-0.71331.056-0.0302-0.21081.68470.30591.23416.736826.8815-105.2899
364.93611.5774-0.22645.2717-5.62956.47370.38351.07570.45481.6753-0.6281-0.4753-0.28570.1347-0.39491.772-0.01150.04960.5869-0.06760.8486-2.549818.1874-100.4444
372.70980.92981.15915.3228-0.05665.11250.6463-0.69210.02830.8704-0.0524-1.0840.54460.8493-0.37420.64650.0736-0.05810.7822-0.0090.728-0.925521.4653-114.2526
385.69393.62913.12273.57850.89892.796-0.32460.2850.31260.38661.2140.61820.74220.4456-0.02930.6688-0.0372-0.01811.03460.11470.6069-17.680541.8061-108.0333
394.1308-0.36991.31174.97311.26545.63630.0191.0051-0.00762.1319-0.0059-0.19460.42951.0432-0.04780.9332-0.87420.19330.84930.7068-0.1053-4.273743.9295-102.0426
403.2471-0.4911-2.07712.6041-0.55444.9666-0.3632-0.7875-0.7780.23070.58521.11940.52870.6474-0.39230.36350.0142-0.00090.63330.07920.3558-21.858917.553-40.0798
417.46090.9954-7.74073.0224-0.10858.3674-0.72561.1367-1.08190.13880.0206-0.29551.30091.11020.44830.45720.25880.07390.94050.05510.34-9.270712.4821-54.9848
427.67121.63941.08017.59182.31535.5618-0.41330.15410.40030.4872-0.25070.4381-0.68190.4380.74020.5786-0.0393-0.0160.7389-0.01460.3052-16.257927.17-61.7749
432.4084-1.7656-2.95659.9739-2.00567.1428-0.7695-0.76231.4352-0.77360.4807-0.63970.0799-0.11170.02880.8973-0.4581-0.01341.5932-0.27810.6771-10.870935.0764-56.1569
449.9102-7.1734-3.45255.95330.87154.5955-0.206-1.09111.9763-0.83150.0039-2.0202-1.51662.9628-0.0060.765-0.1524-0.03251.4447-0.05390.4888-3.087629.372-61.3324
451.5285-0.13010.74582.4769-2.80555.2895-0.1935-0.17510.2626-0.5988-0.5848-0.33680.00561.5177-3.05890.3993-0.07950.25431.41360.11880.2983-7.993328.5423-70.0314
463.4280.94.42052.75591.87596.21040.2079-0.936-0.40461.29510.6052.5251-0.06920.5983-0.42870.9243-0.23050.07770.96520.05360.7286-12.292743.8443-70.7738
470.92190.074-0.36720.8099-1.16832.66750.5133-0.2465-0.39610.3513-0.55390.0306-0.14980.30090.0840.53390.0048-0.07820.6935-0.01420.3781-19.600815.9697-60.8588
483.25991.06961.17513.9312.08091.8101-0.0246-0.15670.4005-0.6755-0.30010.7803-0.1058-0.20830.3160.31740.1101-0.06720.4480.06780.3914-31.457822.6046-50.7495
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 26 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 49 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 50 through 73 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 74 through 88 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 89 through 106 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 107 through 120 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 121 through 139 )A0
8X-RAY DIFFRACTION8chain 'E' and (resid 3 through 26 )E0
9X-RAY DIFFRACTION9chain 'E' and (resid 27 through 49 )E0
10X-RAY DIFFRACTION10chain 'E' and (resid 50 through 73 )E0
11X-RAY DIFFRACTION11chain 'E' and (resid 74 through 139 )E0
12X-RAY DIFFRACTION12chain 'F' and (resid 1 through 26 )F0
13X-RAY DIFFRACTION13chain 'F' and (resid 27 through 49 )F0
14X-RAY DIFFRACTION14chain 'F' and (resid 50 through 94 )F0
15X-RAY DIFFRACTION15chain 'F' and (resid 95 through 118 )F0
16X-RAY DIFFRACTION16chain 'F' and (resid 119 through 139 )F0
17X-RAY DIFFRACTION17chain 'H' and (resid 1 through 26 )H0
18X-RAY DIFFRACTION18chain 'H' and (resid 27 through 42 )H0
19X-RAY DIFFRACTION19chain 'H' and (resid 43 through 60 )H0
20X-RAY DIFFRACTION20chain 'H' and (resid 61 through 73 )H0
21X-RAY DIFFRACTION21chain 'H' and (resid 74 through 88 )H0
22X-RAY DIFFRACTION22chain 'H' and (resid 89 through 139 )H0
23X-RAY DIFFRACTION23chain 'D' and (resid 1 through 16 )D0
24X-RAY DIFFRACTION24chain 'D' and (resid 17 through 49 )D0
25X-RAY DIFFRACTION25chain 'D' and (resid 50 through 104 )D0
26X-RAY DIFFRACTION26chain 'D' and (resid 105 through 139 )D0
27X-RAY DIFFRACTION27chain 'C' and (resid 1 through 43 )C0
28X-RAY DIFFRACTION28chain 'C' and (resid 44 through 60 )C0
29X-RAY DIFFRACTION29chain 'C' and (resid 61 through 73 )C0
30X-RAY DIFFRACTION30chain 'C' and (resid 74 through 106 )C0
31X-RAY DIFFRACTION31chain 'C' and (resid 107 through 120 )C0
32X-RAY DIFFRACTION32chain 'C' and (resid 121 through 139 )C0
33X-RAY DIFFRACTION33chain 'B' and (resid 1 through 31 )B0
34X-RAY DIFFRACTION34chain 'B' and (resid 32 through 42 )B0
35X-RAY DIFFRACTION35chain 'B' and (resid 43 through 49 )B0
36X-RAY DIFFRACTION36chain 'B' and (resid 50 through 60 )B0
37X-RAY DIFFRACTION37chain 'B' and (resid 61 through 106 )B0
38X-RAY DIFFRACTION38chain 'B' and (resid 107 through 120 )B0
39X-RAY DIFFRACTION39chain 'B' and (resid 121 through 139 )B0
40X-RAY DIFFRACTION40chain 'G' and (resid 1 through 15 )G0
41X-RAY DIFFRACTION41chain 'G' and (resid 16 through 30 )G0
42X-RAY DIFFRACTION42chain 'G' and (resid 31 through 49 )G0
43X-RAY DIFFRACTION43chain 'G' and (resid 50 through 60 )G0
44X-RAY DIFFRACTION44chain 'G' and (resid 61 through 73 )G0
45X-RAY DIFFRACTION45chain 'G' and (resid 74 through 81 )G0
46X-RAY DIFFRACTION46chain 'G' and (resid 82 through 88 )G0
47X-RAY DIFFRACTION47chain 'G' and (resid 89 through 118 )G0
48X-RAY DIFFRACTION48chain 'G' and (resid 119 through 139 )G0

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