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- PDB-9c5h: Trypanosoma cruzi beta-3-HBDH structure in complex with NADPH and... -

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Basic information

Entry
Database: PDB / ID: 9c5h
TitleTrypanosoma cruzi beta-3-HBDH structure in complex with NADPH and malonate
ComponentsHydroxybutyrate dehydrogenase
KeywordsOXIDOREDUCTASE / Trypanosoma cruzi / NADPH / malonate / beta-3-Hydroxybutyrate dehydrogenase
Function / homology
Function and homology information


3-hydroxybutyrate dehydrogenase activity / monocarboxylic acid metabolic process / 3-oxoacyl-[acyl-carrier-protein] reductase / lipid metabolic process
Similarity search - Function
3-hydroxybutyrate dehydrogenase / : / short chain dehydrogenase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
MALONATE ION / Chem-NDP / DI(HYDROXYETHYL)ETHER / 3-oxoacyl-[acyl-carrier-protein] reductase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsHashimoto, H. / Debler, E.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI165840 United States
CitationJournal: To Be Published
Title: Trypanosoma cruzi D-3-hydroxybutyrate dehydrogenase (HBDH) is NADP-dependent enzyme.
Authors: Hashimoto, H. / Debler, E.W.
History
DepositionJun 6, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hydroxybutyrate dehydrogenase
B: Hydroxybutyrate dehydrogenase
C: Hydroxybutyrate dehydrogenase
D: Hydroxybutyrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,58523
Polymers114,4684
Non-polymers4,11719
Water15,349852
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)120.575, 81.525, 121.324
Angle α, β, γ (deg.)90.000, 107.400, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11C-420-

HOH

21D-541-

HOH

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Hydroxybutyrate dehydrogenase


Mass: 28617.025 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: genomic DNA / Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Strain: Sylvio X10/1 / Gene: C4B63_13g310 / Plasmid: pED624 / Details (production host): His-3C-TcHBDH / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): RIL-codon plus / References: UniProt: A0A2V2VPF1

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Non-polymers , 5 types, 871 molecules

#2: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H2O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 852 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.49 Å3/Da / Density % sol: 50.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1 M Sodium Citrate, pH 5.6, 2% Tacsimate, pH 5.0, 16% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 13, 2022
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.59→29.66 Å / Num. obs: 149409 / % possible obs: 99.1 % / Redundancy: 6.6 % / Biso Wilson estimate: 24.87 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.09 / Net I/σ(I): 21.4
Reflection shellResolution: 1.59→1.65 Å / Redundancy: 5.5 % / Rmerge(I) obs: 1.329 / Mean I/σ(I) obs: 1.41 / Num. unique obs: 14345 / CC1/2: 0.64 / % possible all: 95.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.59→29.66 Å / SU ML: 0.1964 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.554
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1658 1990 1.34 %random
Rwork0.1446 147036 --
obs0.1449 149026 98.65 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.47 Å2
Refinement stepCycle: LAST / Resolution: 1.59→29.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7759 0 267 853 8879
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00818196
X-RAY DIFFRACTIONf_angle_d1.018911132
X-RAY DIFFRACTIONf_chiral_restr0.05491302
X-RAY DIFFRACTIONf_plane_restr0.00811419
X-RAY DIFFRACTIONf_dihedral_angle_d13.43512933
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.59-1.630.33771300.32169657X-RAY DIFFRACTION91.3
1.63-1.670.29511390.273410272X-RAY DIFFRACTION97.14
1.67-1.720.27391400.236210440X-RAY DIFFRACTION98.13
1.72-1.780.23291420.202310449X-RAY DIFFRACTION98.39
1.78-1.840.20621420.186410468X-RAY DIFFRACTION98.89
1.84-1.910.21271410.186410519X-RAY DIFFRACTION98.93
1.91-20.21731420.15610502X-RAY DIFFRACTION99.23
2-2.110.14951440.147810575X-RAY DIFFRACTION99.56
2.11-2.240.1891430.137910625X-RAY DIFFRACTION99.72
2.24-2.410.1551440.134510614X-RAY DIFFRACTION99.81
2.41-2.650.18411450.133110652X-RAY DIFFRACTION99.94
2.65-3.040.18461460.137910721X-RAY DIFFRACTION99.99
3.04-3.820.15181450.132610692X-RAY DIFFRACTION100
3.82-29.660.11961470.125910850X-RAY DIFFRACTION99.94
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)
12.76315658645-1.239400194830.4831640429263.26808254417-0.3900991122492.636629079250.007842490243610.2947000536270.075445572949-0.1621441365610.02829325647210.0895927350906-0.2711546008920.0218852161739-0.06948885279920.395926336464-0.0870586527261-0.006951958234450.2797959888570.03055072103490.171635548784-33.022013333216.777472109611.1712966997
26.89411148281-3.056535141311.899244749212.25137313341-1.127675689322.169007243620.04509599186850.336144458984-0.118816839194-0.250239653646-0.05034740238840.00446123151164-0.2331733138360.0103891656884-0.005289059677470.503358490065-0.1268029837370.008759188241580.3513879743930.06045969304250.247000933985-30.363438727920.54056305597.84814149672
37.31184177905-4.93507243131-1.384250317847.320649985531.196582307481.73012029209-0.2418305334410.3198952962750.703773912770.3702124415580.0531123630887-0.601588004861-0.7760038662910.353349860786-0.01498829932120.62614056436-0.218543505959-0.04489416456470.3838580093960.0726079785940.338130729967-21.95714045925.599159604716.8982996621
42.68249988091-2.59846960618-0.6753404565973.884101907940.5987454027161.39121186281-0.02624673378750.173313904780.0251610247278-0.193292857778-0.0202977597796-0.243886108779-0.2025699878990.2831142178780.1581732246240.369891121955-0.1263967236840.04496241120020.3936024029620.005679255977960.254892833339-20.15779815476.4070104834914.8569498788
51.94806595082-1.1487958012-0.6888132907322.535622728850.7844864292632.498380298340.06091198401420.2520155879120.171358469368-0.225041803253-0.0951281468965-0.332259158725-0.5329697925320.283907104051-0.04021644854260.442647171911-0.1738041777040.002916976744210.3503999941710.03496586194870.288142117075-18.713437636713.364247551422.0991311743
60.800213645911-0.294916435388-0.0268282620811.23165866093-0.09337098130371.54000678928-0.03835771999830.149769888686-0.0312838708381-0.1166198127370.0366086676279-0.0767035465075-0.2005448653410.1687279396480.02327151462640.297143470688-0.1046522338210.01576498898760.266200460979-0.0140425420770.207758022079-26.41544277164.3298833859122.9125568899
77.10417227836-5.10104238018-5.46279650596.461775241855.610708139665.709243884850.2256803488490.2350351663150.0483314317171-0.9424774098360.229152248152-0.340478908173-0.5419771213810.733713043313-0.4308778686310.536777791825-0.1064931151730.0426010728620.526647383746-0.069383209370.23337039385-22.9655904315-5.227746159380.909379672403
84.0815042872-0.473552081433-5.43381079346.28667491052-2.872830899989.413555403260.06200026485240.0685633225616-0.32717229889-0.242336766092-0.3804745850020.2216225933530.0557495751865-0.5936303002880.3074668847740.460111938757-0.0038069993417-0.02599298676440.459015258472-0.130890286190.276212084354-28.7652365867-11.95569252760.744715449099
90.71789954952-0.412107521520.1527588779923.422715994910.9884179840222.1530703546-0.01314525234180.145030199834-0.0301295391106-0.2213842105540.05593487318170.0496691570026-0.105599237618-0.0524456025314-0.04967334007180.240498502322-0.08399916377660.01437848351610.277142445902-0.01374602621210.182976819088-35.90781269450.5522102627819.2277833143
105.328487321870.32580066544-0.9859271303152.670157430630.3305986638884.93104246883-0.045771027467-0.07565349540850.120490533015-0.06607525279970.02367472973670.473584810563-0.217569344387-0.0496146615604-0.009699130151780.1696131971760.0321773421886-0.03071043497630.284588345740.05339374981040.36567415941-58.72208767050.4845600985730.5054161532
115.48565501434-5.568606442872.305514329239.33616689554-3.619941884593.093008209320.0273947445026-0.1014669875610.03772610676410.0458457468512-0.0184469104980.489378262017-0.146373865009-0.0433354970244-0.02955924249560.180088768586-0.0006761260943150.0193643458990.3319987693260.02971022679760.409189635998-63.8924448802-1.0331299476832.4699743776
122.8052431251-1.767039819042.873943628654.03732616265-3.191459392885.517579705370.1103658513950.0934723771811-0.471243464566-0.5020057151530.3550122839380.7798819264220.587532247545-0.550857384984-0.4317011021050.295016579135-0.0942814356216-0.01905807966390.4630763373680.0644757972950.585249055029-63.8503582345-13.593086389228.0689737014
131.73070950274-0.6683833099371.851150403231.34501640647-0.9033152908873.67129979258-0.147179664553-0.237879074375-0.08630346399310.06011600925690.1955356838550.186398811092-0.191128808606-0.446128474951-0.01518760580270.199856206009-0.0140649966580.03857117266840.3388805225470.03623574063810.308900200563-48.6575387456-9.7701836897239.4354244071
141.47585624620.09311235174640.6503901748661.33687388836-0.04353353440222.66728404906-0.0380925344843-0.00644553654553-0.1161928447-0.07747332265810.1547539658750.208562837134-0.0576924442968-0.22053616732-0.1186362475560.173140863136-0.02463066165540.001310712950710.2509938472520.01234738824850.269837875846-45.4986052291-10.82999860131.7669261375
158.600282677851.933144767724.667927065253.579859006013.291143972669.357222336960.0107349845031-1.07019560184-0.004263661016751.49508031292-0.2817799677640.982351799586-0.106659674768-0.7633495531340.1921798803650.7509784200310.1110249942920.1848114428990.612900702521-0.003656571785320.459549042635-45.23247447031.5440382884353.5789452489
166.33490374753-0.485857405263-0.9077538899293.377070994714.108120506775.004482868010.103659840782-1.212337688520.8197005873740.898260415924-0.3202374781770.290566367226-1.30233851021-0.0797941991629-0.04824226536620.9649850556070.06990738931530.0412992796410.548754046083-0.1352266995870.380063038565-39.97477889418.3926522246453.7283345794
172.146111252240.03026586655380.7870497218711.83269262153-0.01363321238321.79897501926-0.1102491216660.03240290408210.03028148195270.02890990656730.130557065020.135197350414-0.207166324814-0.104552473655-0.02977311654310.261984674213-0.03379161982270.02352409894950.2189049694370.02055998702060.206722564047-40.43248773662.8554883581830.8431911908
180.391480441523-0.770285754102-0.8686729286143.11060769427-0.01683947784124.889087530080.05291734347850.0162290889147-0.51956312557-0.2073967477440.0386680964263-0.1971225614350.3274585200670.0588014505203-0.08576673507870.2310346894110.0196431749535-0.03975321668190.179009356535-0.01813962604350.510481743132-23.5543842836-35.687872655243.6313725778
195.78193160974-1.171093273120.2714164389973.26490295396-0.2552362175252.000062643070.01351150224320.049388022008-0.885364436861-0.1542249231780.015280637132-0.05858016753770.3804309244450.0494742058448-0.02133352172250.285602971722-0.0279074767362-0.03408561128870.2305989233730.01510192070190.536926780373-26.5714133447-40.016255579645.6520572737
202.03079890852-1.899799492091.749266313293.759826126840.1631976172854.2857165008-0.161859434544-0.765685446751-0.6500368053280.3946622646370.2151040217990.2499217572480.00794774421469-0.4551736043-0.08985242737320.273211167556-0.04613724966070.007881896274330.3683395540390.1127529690840.465514578101-34.1574003927-34.035445137354.4093517902
211.20641639401-0.000232027659170.7793757943790.943312376764-0.2520635348111.674616703520.0522395393267-0.019019933255-0.27687941312-0.04290797634780.09134760928510.02118564142970.133705970843-0.0592549296448-0.1566426566930.18624840879-0.0280299060724-0.004834464652810.207661478909-0.01427172603060.304154116388-33.3987394758-22.360985043739.7342014956
228.694887085971.422917797324.509004919296.148548222492.385049161044.04595281295-0.08396098582490.604903391708-1.14478977587-0.562187345390.3059666176740.4518914300050.822230358243-0.640158752251-0.1582286012310.652902971613-0.134692251254-0.03472957657850.5005973291-0.1960624754930.701853196405-34.5705507142-34.408220249919.2362961551
231.009353034710.9424703798321.984621257247.910822911025.453182288395.79295475254-0.1963802881590.973602107043-0.782285980732-0.6051493404970.444369303408-0.6412357702091.371828605360.424607022186-0.421379072080.801484638227-0.05521998348960.01996703276650.699200476797-0.305553461970.589345484894-28.422080762-32.485489558113.407682914
241.41558507666-0.376544480088-0.009405646118771.51012058863-0.0957158769413.227807022490.02328940213660.211735198793-0.270865248515-0.1438768310140.0459590104285-0.146904540870.1399390452630.236419045789-0.0850655819870.180702864512-0.0314460719180.02308727720030.250594073973-0.07155578522150.337843692342-20.6100338165-21.28418175832.6024977224
253.997422022142.0996758017-0.2467308430822.00233239376-0.6511205251892.24750920891-0.0175169026583-0.0402574700018-0.1630652220760.163096547502-0.152584713241-0.752605848676-0.1142631474230.555949004550.05052301300350.217813308706-0.0577874222086-0.01555290462260.556670648365-0.00385619327930.5483486305012.46808642882-11.212878715336.6681388133
264.21305278142-0.56010983321.512436353194.07377310611-1.511967541422.41865819014-0.001700958986620.0871065546514-0.2664013385150.1052309084-0.154446189383-0.729264935342-0.1812835400110.8722040814060.157137919590.253813792718-0.1154425060910.005943784469830.698911706493-0.01707850267990.6380313673267.65730288611-9.2312753378936.1907593836
273.09352352612-2.682203087420.2558439595336.17311463515-0.2116352292071.398617096040.04993098148210.830806877447-0.337368660081-0.757962860642-0.299920464908-0.692697322503-0.118237226380.5578980503880.2526393549820.322295426281-0.171823433080.1487332662990.953965655262-0.04950382238030.6277142525647.24839768594-7.521766550122.9118388917
281.00027533589-0.05751826292620.1901168489421.326782641360.02431957215211.25359718408-0.06622217264760.207347387987-0.0452953595171-0.09424348862990.0194248984731-0.375935954787-0.1715661407160.4037786022020.04372194505760.213069107731-0.1142108631790.03957289969650.393572107569-0.02734032802510.305913008345-10.2929751983-3.9920598081328.3932482058
298.14812962382-6.69715656454-6.299705246986.078737449215.21869121815.59446695784-0.182344786315-0.002747296293511.00724602858-0.0005846945757990.493289311414-1.13864362142-1.220069656370.804077514859-0.2995677803790.59743270927-0.149493512862-0.1594113234820.422541776804-0.01443706995290.483112875124-10.39075642149.033314874248.2645746353
308.511214968651.3219431039-1.400588278561.011008189312.100232941146.957630260460.384318392408-0.6186305687990.06968154067021.201559865210.119166062245-0.5482657741690.5138355659810.2076120196-0.3449834281050.730389264598-0.0622502927122-0.1578843339810.353936496073-0.01687484503440.344840749516-15.52387172076.1342012080154.5323403798
311.87014427031-0.2443136373850.067655322651.451330982740.2934756481842.43416417275-0.08190606994650.0607310353627-0.2084812473190.08209439618640.0600202826408-0.209276408147-0.03731280407720.2708986110240.0081056704810.217574711275-0.0631147482445-0.006608655412660.290428327746-0.02347361564960.322866317481-15.8450250434-11.801766675639.5517072145
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 5 through 47 )AA5 - 471 - 43
22chain 'A' and (resid 48 through 71 )AA48 - 7144 - 67
33chain 'A' and (resid 72 through 85 )AA72 - 8568 - 81
44chain 'A' and (resid 86 through 108 )AA86 - 10882 - 104
55chain 'A' and (resid 109 through 137 )AA109 - 137105 - 133
66chain 'A' and (resid 138 through 195 )AA138 - 195134 - 191
77chain 'A' and (resid 196 through 209 )AA196 - 209192 - 205
88chain 'A' and (resid 210 through 223 )AA210 - 223206 - 219
99chain 'A' and (resid 224 through 266 )AA224 - 266220 - 262
1010chain 'B' and (resid 5 through 47 )BB5 - 471 - 43
1111chain 'B' and (resid 48 through 71 )BB48 - 7144 - 67
1212chain 'B' and (resid 72 through 85 )BB72 - 8568 - 81
1313chain 'B' and (resid 86 through 108 )BB86 - 10882 - 104
1414chain 'B' and (resid 109 through 195 )BB109 - 195105 - 191
1515chain 'B' and (resid 196 through 209 )BB196 - 209192 - 205
1616chain 'B' and (resid 210 through 223 )BB210 - 223206 - 219
1717chain 'B' and (resid 224 through 266 )BB224 - 266220 - 262
1818chain 'C' and (resid 5 through 47 )CH5 - 471 - 43
1919chain 'C' and (resid 48 through 71 )CH48 - 7144 - 67
2020chain 'C' and (resid 72 through 85 )CH72 - 8568 - 81
2121chain 'C' and (resid 86 through 195 )CH86 - 19582 - 191
2222chain 'C' and (resid 196 through 209 )CH196 - 209192 - 205
2323chain 'C' and (resid 210 through 223 )CH210 - 223206 - 219
2424chain 'C' and (resid 224 through 266 )CH224 - 266220 - 262
2525chain 'D' and (resid 6 through 47 )DM6 - 471 - 42
2626chain 'D' and (resid 48 through 71 )DM48 - 7143 - 66
2727chain 'D' and (resid 72 through 85 )DM72 - 8567 - 80
2828chain 'D' and (resid 86 through 195 )DM86 - 19581 - 190
2929chain 'D' and (resid 196 through 209 )DM196 - 209191 - 204
3030chain 'D' and (resid 210 through 223 )DM210 - 223205 - 218
3131chain 'D' and (resid 224 through 266 )DM224 - 266219 - 261

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