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- PDB-2ob0: Human MAK3 homolog in complex with Acetyl-CoA -

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Basic information

Entry
Database: PDB / ID: 2ob0
TitleHuman MAK3 homolog in complex with Acetyl-CoA
ComponentsHuman MAK3 homolog
KeywordsTRANSFERASE / acetyltransferase / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


: / mitotic sister chromatid cohesion, centromeric / N-terminal methionine Nalpha-acetyltransferase NatE / NatA complex / N-terminal protein amino acid acetylation / peptide alpha-N-acetyltransferase activity / histone H4 acetyltransferase activity / establishment of mitotic sister chromatid cohesion / mitotic sister chromatid cohesion / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups ...: / mitotic sister chromatid cohesion, centromeric / N-terminal methionine Nalpha-acetyltransferase NatE / NatA complex / N-terminal protein amino acid acetylation / peptide alpha-N-acetyltransferase activity / histone H4 acetyltransferase activity / establishment of mitotic sister chromatid cohesion / mitotic sister chromatid cohesion / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / nucleolus / extracellular exosome / nucleus / cytoplasm / cytosol
Similarity search - Function
Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETYL COENZYME *A / N-alpha-acetyltransferase 50
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsWalker, J.R. / Schuetz, S. / Antoshenko, T. / Wu, H. / Bernstein, G. / Loppnau, P. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. ...Walker, J.R. / Schuetz, S. / Antoshenko, T. / Wu, H. / Bernstein, G. / Loppnau, P. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Plotnikov, A.N. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Structure of Human MAK3 homolog
Authors: Schuetz, A. / Walker, J.R. / Antoshenko, T. / Wu, H. / Bernstein, G. / Loppnau, P. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Plotnikov, A.N.
History
DepositionDec 18, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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: Human MAK3 homolog
B: Human MAK3 homolog
C: Human MAK3 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0316
Polymers58,6023
Non-polymers2,4293
Water5,963331
1
A: Human MAK3 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3442
Polymers19,5341
Non-polymers8101
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Human MAK3 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3442
Polymers19,5341
Non-polymers8101
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Human MAK3 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3442
Polymers19,5341
Non-polymers8101
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.523, 103.324, 67.328
Angle α, β, γ (deg.)90.00, 106.79, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Human MAK3 homolog / N-acetyltransferase 13


Mass: 19534.098 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NAT13 / Plasmid: pET28-LIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9GZZ1, EC: 2.3.1.88
#2: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 331 / 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: 2.7 Å3/Da / Density % sol: 54.44 %
Crystal growTemperature: 298 K / pH: 7.5
Details: Reservoir: 0.1 M Sodium acetate pH 5.0, 16% PEG3350, 10 mM DTT, 0.1% Dioxane. Protein: 11.8 mg/mL + 3-fold molar excess of ACOA in 20 mM Hepes pH 7.5, 0.1 M NaCl, 2.5 % 1,2-propandiol, and ...Details: Reservoir: 0.1 M Sodium acetate pH 5.0, 16% PEG3350, 10 mM DTT, 0.1% Dioxane. Protein: 11.8 mg/mL + 3-fold molar excess of ACOA in 20 mM Hepes pH 7.5, 0.1 M NaCl, 2.5 % 1,2-propandiol, and 10 mM DTT. Cryo: 75% reservoir + 25% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.97931, 0.97945, 1.00000
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 18, 2006
Details: 1-M LONG, CYLINDRICALLY BENT ULE GLASS MIRROR WITH PT AND PD COATINGS
RadiationMonochromator: CRYO-COOLED SI(111) DOUBLE- CRYSTAL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979311
20.979451
311
ReflectionResolution: 1.8→50 Å / Num. obs: 56481 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rsym value: 0.046 / Net I/σ(I): 28.8
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2 / Rsym value: 0.504 / % possible all: 88.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.959 / SU B: 4.821 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.108 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS, ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS
RfactorNum. reflection% reflectionSelection details
Rfree0.204 2858 5.1 %RANDOM
Rwork0.169 ---
obs0.171 53533 98 %-
all-53533 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.88 Å2
Baniso -1Baniso -2Baniso -3
1-2.29 Å20 Å2-1.44 Å2
2---1.49 Å20 Å2
3----1.63 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3828 0 153 331 4312
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224062
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5182.0025503
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4365473
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.224.456193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.54615715
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5451522
X-RAY DIFFRACTIONr_chiral_restr0.1020.2600
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023008
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2080.21614
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.22792
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2304
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1630.238
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.120.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8432444
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.62743819
X-RAY DIFFRACTIONr_scbond_it3.43651838
X-RAY DIFFRACTIONr_scangle_it5.00771684
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 174 -
Rwork0.248 3456 -
obs--85.78 %
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)
120.719219.604-11.214824.6651-13.801115.3507-0.27930.36530.349-0.24750.3586-0.7718-0.89630.6419-0.07940.0595-0.13780.03720.06060.01590.09346.9132358.1374-94.3179
211.18883.0456-5.75185.20761.02394.48840.0793-0.2570.40780.4738-0.06970.61220.09210.0988-0.00960.1087-0.01350.09790.0413-0.00980.115835.9093352.0857-79.5533
332.220815.83518.926328.88268.513714.1312-0.31190.09070.80620.1125-0.2811.232-0.765-0.27590.59290.03270.01940.11630.0447-0.00220.169130.3517345.9034-84.1829
44.1938-4.6932-1.393610.01972.85989.43540.0364-0.0449-0.65620.2046-0.0730.70260.2002-0.10430.03660.0027-0.05470.04490.04860.0170.177533.2754338.3772-88.2079
58.29458.44474.283622.77629.312314.08920.2395-0.2013-0.35171.2048-0.11240.16840.3648-0.2104-0.12710.1169-0.02340.15480.04370.05110.090234.2875339.4356-76.0487
63.5353-0.6273.26565.4531-2.66078.18040.0226-0.16540.07810.31730.06510.038-0.1513-0.0313-0.08770.0968-0.01140.0650.1097-0.02670.110540.6805351.1132-84.5439
77.5664-6.53786.70328.1372-7.46868.52570.0467-0.3989-0.4170.34190.15640.15250.42760.113-0.2030.16020.08970.00170.0750.01550.016847.4709337.3357-77.6745
82.317-1.23431.61472.7594-1.37162.9464-0.0154-0.0534-0.02810.06780.02970.11930.0501-0.0627-0.01430.08070.00320.02820.1276-0.01710.106844.2956341.8753-89.5501
99.4586-1.0511.65717.1329-1.905716.0183-0.0383-0.08170.14220.66410.0834-0.4965-0.34040.5085-0.04510.0501-0.0325-0.02550.1161-0.01670.0753.2963346.8363-82.7796
103.79161.63342.68615.74442.70735.6993-0.14-0.0473-0.04950.40840.05740.06370.18340.34130.08260.08840.02810.03590.1150.00490.082750.4837333.4021-83.2361
1114.0219-1.1293-0.58194.7653-0.46223.197-0.01780.6593-0.1113-0.16910.0181-0.0078-0.02090.1596-0.00040.05690.01980.03980.1254-0.02530.072450.5509335.826-94.8499
125.32695.7543.186344.23421.52255.11030.0843-0.0651-0.46980.47720.0057-0.84660.51010.4185-0.090.0590.06460.00050.1073-0.02940.079754.4302328.9599-87.8802
1329.61-14.2966-7.00996.9033.342610.0759-0.2578-0.4094-0.96260.61840.13450.66810.7614-0.17770.12330.1714-0.06720.1246-0.02740.01320.217843.7781321.6857-85.7908
1435.83642.1278-3.69351.8489-6.036837.4875-0.1760.12-0.67530.22180.19892.14371.4356-0.6524-0.0229-0.0322-0.03480.1103-0.0793-0.00480.447435.87324.1343-88.8847
1515.210712.57816.023516.31066.05186.44170.0310.1697-0.21250.420.1184-0.16470.34550.4387-0.14940.07250.03640.03350.1335-0.02050.08951.6938330.0967-86.3914
165.6973-2.9658-0.547914.0332-5.3042.8818-0.12190.41770.1495-0.9565-0.064-0.22680.3111-0.05790.18590.1415-0.0361-0.02520.15440.0414-0.055224.8161343.9021-127.909
174.8322-0.3727-4.19834.7528-0.722548.9838-0.27710.32110.159-0.4848-0.11410.3138-0.2493-1.76370.39120.03730.0229-0.14080.06860.03130.127314.5598352.514-124.6415
184.07780.61094.312813.20641.247912.0807-0.2896-0.34820.34360.268-0.05550.1834-0.4359-0.38120.34510.01340.041-0.03460.073-0.00140.130918.4392351.6903-112.7102
196.22714.7802-8.03838.8229-1.968726.0091-0.27940.28570.6674-0.3128-0.10860.1543-1.1447-0.65260.3880.05740.0823-0.1449-0.02080.08770.213418.6558361.4522-119.6878
202.58195.7341-1.413720.2227-1.2343.9328-0.11420.28510.2173-0.35520.02890.2296-0.21830.08590.08530.0958-0.0295-0.05040.12560.07690.059724.1828348.2821-126.1285
2111.5412.64220.619618.60921.48870.1711-0.11870.14030.6051-0.141-0.06160.2825-0.15150.060.18040.1116-0.058-0.0860.06570.08620.104926.5797354.1511-120.2698
2234.781615.183312.722722.483214.34779.5312-0.5476-0.38011.99230.3281-0.67661.0229-1.77240.63961.22420.2768-0.2981-0.13130.0760.04880.239838.9691367.8224-116.1094
233.66062.8740.37295.8308-0.52662.3633-0.25140.1960.3115-0.15940.14830.2079-0.18520.03480.10320.074-0.0173-0.02830.1030.03820.11528.1382351.2129-115.6641
245.29374.0465-0.234312.866-3.8463.4168-0.09670.1340.12150.0011-0.1275-0.02530.12360.22020.22410.0638-0.02680.01680.12380.00520.050231.7444343.3949-119.0838
259.07215.2441-7.145731.1857-14.190717.9518-0.55070.6894-0.1401-1.1362-0.0896-0.6518-0.03830.78840.64030.0097-0.13420.00050.17350.1240.006639.5787353.8507-125.6402
263.91641.2919-2.17462.531-1.87778.8171-0.22830.19680.23620.0001-0.0241-0.1393-0.36540.20380.25240.0661-0.047-0.04150.08290.05310.130835.631357.7533-112.2938
2711.32830.15882.10994.05860.55795.37560.02770.0062-0.31420.0908-0.0302-0.04720.25040.10750.00250.0877-0.0104-0.01590.10050.02970.079534.8276346.3943-108.0032
284.74720.7919-1.824111.140215.762424.1507-0.2536-0.17670.3799-0.29040.2854-0.3427-0.86180.6622-0.03180.0891-0.1102-0.0620.11720.0620.081640.0767355.3206-106.7794
2916.2583-2.8503-3.00087.1270.60795.5613-0.2877-0.21380.35250.3166-0.0140.4208-0.7401-0.77570.30170.08590.0979-0.02240.1085-0.04610.04626.5625359.8462-101.0473
3013.723-5.5816-9.57136.29552.358630.81890.06420.12290.4724-0.2745-0.1961-0.6275-0.92072.1780.1319-0.0089-0.128-0.00690.22270.08420.099942.9588356.5619-114.1722
318.8715-1.15276.82547.6988-3.983416.14440.01790.6298-0.3327-1.11350.12550.25090.67110.3249-0.14340.0896-0.02240.01450.0667-0.04270.103950.4643366.0301-94.7952
323.63350.41360.029120.9232.28923.2605-0.07080.0501-0.3343-0.29040.1276-0.9950.23880.6342-0.0569-0.02980.0488-0.010.12360.04440.167660.6956366.449-84.7602
330.9165-1.98640.92548.0349-6.84729.6276-0.01-0.2858-0.01770.27430.0326-0.241-0.31160.367-0.0225-0.0071-0.0176-0.07210.09590.02450.098657.7125372.3809-76.3903
3415.2446-0.92898.7257.60190.58167.90990.2416-0.3268-1.00770.52140.0138-0.25660.68160.006-0.25540.12780.03070.03740.01540.07480.139552.3516359.8916-78.3636
353.58780.8589-2.68032.3956-1.64866.6466-0.0802-0.2508-0.05270.13390.04690.05710.13670.01950.03330.09510.00410.02370.09470.0330.14148.0624367.5371-82.1851
362.14230.9033-1.80322.7021-1.42514.1434-0.04970.0430.040.0564-0.0117-0.1501-0.05350.03010.06140.07150.0130.01540.10590.02160.143946.971374.2116-84.7663
377.15388.2171-5.724413.1648-7.65267.9963-0.06790.0365-0.3234-0.0476-0.0380.29270.1979-0.02830.10590.0490.00360.0350.0785-0.01760.133439.0963364.5184-85.1501
383.92482.6450.34685.56192.77141.7346-0.1489-0.1875-0.10120.19070.0719-0.0536-0.0324-0.01440.07710.10850.00910.01750.0868-0.00310.098340.7189373.1702-74.4043
399.15980.1690.54695.01861.94947.0988-0.05060.10090.67530.05060.1091-0.2424-0.44570.1782-0.05850.10470.01830.01720.05390.01070.113642.173382.6924-82.4803
409.1749-0.72992.4421.4426-6.69844.84130.11290.2478-0.0735-0.1571-0.27170.66880.2276-0.2720.15880.04250.01910.01310.138-0.03530.113134.8669378.3529-81.7826
4119.8168-0.43352.23842.52560.42283.8567-0.004-1.31950.10450.70760.051-0.22440.03790.1703-0.0470.13970.0132-0.06040.0344-0.0516-0.007644.0253381.5843-68.1919
4225.1448-11.1879-2.13188.7484-7.85720.7449-0.4944-0.33870.87321.8640.7315-1.6027-0.11961.7529-0.23710.0352-0.1399-0.24890.2016-0.27390.2654.198385.7707-69.492
4314.678912.97565.210721.68067.85227.7657-0.2211-0.09910.07250.13840.05410.2054-0.0394-0.04930.1670.10530.0360.01450.0762-0.00750.100438.0158376.8696-73.951
4443.220810.6303-24.29267.1313-5.742613.66581.4929-2.84011.5326-0.35420.25320.2485-0.32781.4167-1.74610.008-0.04650.0550.22350.09340.233822.9122365.5028-69.6233
4539.8409-16.655815.463823.2445-6.33814.7273-0.1805-0.3795-0.79811.17630.17430.1492-0.25570.12930.00620.0709-0.084-0.09590.02890.13550.05659.7252365.6566-66.6299
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 72 - 8
2X-RAY DIFFRACTION2AA8 - 169 - 17
3X-RAY DIFFRACTION3AA17 - 2118 - 22
4X-RAY DIFFRACTION4AA22 - 2923 - 30
5X-RAY DIFFRACTION5AA30 - 4031 - 41
6X-RAY DIFFRACTION6AA41 - 5442 - 55
7X-RAY DIFFRACTION7AA55 - 6956 - 70
8X-RAY DIFFRACTION8AA70 - 9071 - 91
9X-RAY DIFFRACTION9AA91 - 10392 - 104
10X-RAY DIFFRACTION10AA104 - 116105 - 117
11X-RAY DIFFRACTION11AA117 - 128118 - 129
12X-RAY DIFFRACTION12AA129 - 133130 - 134
13X-RAY DIFFRACTION13AA134 - 138135 - 139
14X-RAY DIFFRACTION14AA139 - 144140 - 145
15X-RAY DIFFRACTION15AA145 - 154146 - 155
16X-RAY DIFFRACTION16BB4 - 125 - 13
17X-RAY DIFFRACTION17BB13 - 2114 - 22
18X-RAY DIFFRACTION18BB22 - 2923 - 30
19X-RAY DIFFRACTION19BB30 - 4031 - 41
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