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- PDB-8g4p: Crystal structure of the peanut allergen Ara h 2 bound by two neu... -

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Basic information

Entry
Database: PDB / ID: 8g4p
TitleCrystal structure of the peanut allergen Ara h 2 bound by two neutralizing antibodies 13T1 and 13T5
Components
  • 13T1 Fab light chain
  • 13T5 Fab heavy chain
  • 13T5 Fab light chain
  • 13t1 Fab heavy chain
  • Ara h 2 allergen
KeywordsALLERGEN / allergy / antibody / peanut / epitope / paratope
Function / homologyNapin/ 2S seed storage protein/Conglutin / Protease inhibitor/seed storage/LTP family / Plant lipid transfer protein / seed storage protein / trypsin-alpha amylase inhibitor domain family / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily / nutrient reservoir activity / Ara h 2 allergen
Function and homology information
Biological speciesHomo sapiens (human)
Arachis hypogaea (peanut)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsPedersen, L.C. / Mueller, G.A. / Min, J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)1ZIAES102906 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)1ZICES102645 United States
CitationJournal: Clin Exp Allergy / Year: 2024
Title: Design of an Ara h 2 hypoallergen from conformational epitopes.
Authors: Min, J. / Keswani, T. / LaHood, N.A. / Lytle, I.R. / Marini-Rapoport, O. / Andrieux, L. / Sneed, S.L. / Edwards, L.L. / Petrovich, R.M. / Perera, L. / Pomes, A. / Pedersen, L.C. / Patil, S.U. / Mueller, G.A.
History
DepositionFeb 10, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 31, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: 13t1 Fab heavy chain
D: 13T1 Fab light chain
A: 13T5 Fab heavy chain
B: 13T5 Fab light chain
E: Ara h 2 allergen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,68223
Polymers112,4565
Non-polymers1,22618
Water4,450247
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)136.302, 136.794, 96.819
Angle α, β, γ (deg.)90.000, 127.340, 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
11B-786-

HOH

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Components

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Antibody , 4 types, 4 molecules CDAB

#1: Antibody 13t1 Fab heavy chain


Mass: 24478.322 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): ExpiCHO-S / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody 13T1 Fab light chain


Mass: 23665.354 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): ExpiCHO-S / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody 13T5 Fab heavy chain


Mass: 25040.055 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): ExpiCHO-S / Production host: Cricetulus griseus (Chinese hamster)
#4: Antibody 13T5 Fab light chain


Mass: 23396.951 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)

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Protein / Sugars , 2 types, 2 molecules E

#5: Protein Ara h 2 allergen


Mass: 15875.369 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arachis hypogaea (peanut) / Gene: Ara h 2 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A445BYI5
#9: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / 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 , 4 types, 264 molecules

#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#8: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 247 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.19 Å3/Da / Density % sol: 61.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1M Tris pH 8.5 0.2M Lithium Sulfate 40% Peg400 / Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 65663 / % possible obs: 98.1 % / Redundancy: 3.6 % / Biso Wilson estimate: 48.6 Å2 / CC1/2: 0.993 / Rpim(I) all: 0.04 / Rrim(I) all: 0.076 / Rsym value: 0.064 / Net I/σ(I): 7.2
Reflection shellResolution: 2.25→2.29 Å / Num. unique obs: 3233 / CC1/2: 0.782 / Rsym value: 0.636

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→42.55 Å / SU ML: 0.2907 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.0593
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2175 1978 3.04 %
Rwork0.1887 63157 -
obs0.1896 65135 97.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.49 Å2
Refinement stepCycle: LAST / Resolution: 2.25→42.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7126 0 65 247 7438
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00577362
X-RAY DIFFRACTIONf_angle_d0.820910049
X-RAY DIFFRACTIONf_chiral_restr0.0521154
X-RAY DIFFRACTIONf_plane_restr0.00711300
X-RAY DIFFRACTIONf_dihedral_angle_d13.45382545
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.30.30091340.26664361X-RAY DIFFRACTION94.37
2.3-2.370.29131420.2564442X-RAY DIFFRACTION96.57
2.37-2.440.30281370.26034489X-RAY DIFFRACTION97
2.44-2.510.28011390.23254486X-RAY DIFFRACTION97.31
2.51-2.60.26941430.224531X-RAY DIFFRACTION97.54
2.6-2.710.24911420.20384527X-RAY DIFFRACTION97.99
2.71-2.830.22981420.224577X-RAY DIFFRACTION98.33
2.83-2.980.2671430.23194527X-RAY DIFFRACTION98.19
2.98-3.170.32031350.21534290X-RAY DIFFRACTION92.48
3.17-3.410.23171430.20084541X-RAY DIFFRACTION98.07
3.41-3.750.18651450.18364615X-RAY DIFFRACTION99.42
3.75-4.30.19411460.15624656X-RAY DIFFRACTION99.4
4.3-5.410.15291450.13934604X-RAY DIFFRACTION98.57
5.41-42.550.21581420.1924511X-RAY DIFFRACTION95.64
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)
14.33370817106-1.86816683670.8285108159282.00870204866-0.6604304722993.972942900650.0129809998185-0.619598273255-0.7194791491460.6288388927340.322676735737-0.007072621100380.596245598045-0.529954851031-0.2416878348540.577037503587-0.13148540866-0.0710909779470.7012094001340.1173290217460.56527318981515.5212069281-3.9632767944972.799822939
23.82476984843-0.534012200029-0.3157652517246.65955048233-0.06638575888425.227507524640.0931338041955-0.490659931768-0.441369281478-0.2287608869330.1303700702220.1118908625650.263632483732-0.781825390852-0.2082342817220.349215384427-0.0854690798607-0.07078742297180.5701682737510.03263006247360.38949101051613.8786075832.1352724741263.2301638754
35.17764037596-0.113527956426-1.834851513644.845856531931.446654825467.555289404740.243891251599-0.160929545393-0.628531124636-0.276618151742-0.1437033844370.3022972006590.759390651119-1.04717438407-0.01774375999850.567630757458-0.197863971106-0.1866599003970.6507530792560.02989782976140.61082883473410.2385074502-3.7990455824963.3963137251
43.47370454666-1.249226587252.015475516156.46432687817-3.274896328185.292796705090.40996900213-0.488382290342-0.646974295246-0.425698740974-0.1744778998030.1547072626110.484934581839-0.44135496544-0.1235920343610.405738527266-0.0636292816484-0.04977677317080.504345328656-0.004193811137650.44245473652218.4548708992.7984363553863.8297767443
52.930883781730.6415499686293.593888785716.405272700232.33562889958.18821120619-0.249768283511-1.113577836-0.7523789117420.1281593484690.643419870259-0.241475672770.00224396584294-0.138503466124-0.2958286481320.497239171904-0.03395571371220.09353142652591.257852044510.252072441530.62413261192534.8774692967-8.196396202491.1919327576
63.621086963160.2906005958540.4898541467422.8811555263-1.102343157254.58916302713-0.0983390503583-1.53210982493-0.00478568068650.4965571521050.2828044293460.6736460504130.203929362977-1.04536344392-0.1599872891110.4459850400370.1066670047150.1011604243411.191393725690.1832815572590.58849479396630.7941047129-3.5978738235390.3299136577
76.1128401295-0.9375225496133.166022346932.96823175198-1.554323907112.502700056030.044025823161.14171148735-0.207003001634-0.645236117490.103958910721-0.3393484343880.3508766987930.722371473295-0.2507441452180.5539743939350.02229146381980.1267624411530.655167968804-0.03565129308320.50971439242237.632772950810.054924764657.12753405
87.34669022732-0.8077455604324.68097508344.90963681623-3.070460242684.69140899783-0.126394717183-0.862685147079-0.2485236626630.2592374407890.1119817020520.0537900901689-0.204928114163-0.252822439552-0.01008100466430.3581041576820.07867948945440.05157160134680.523366855365-0.07816080693240.38124668432927.799539264810.693810632564.798294748
96.909267048312.06841995163.598806928954.812871045192.527894568425.22707480627-0.524298146067-0.3773242251381.60246501625-0.440077757737-0.1919433316460.268617126679-0.877628522303-0.4078097546050.871547907770.4614156641250.0736259057236-0.06089973575990.472057035424-0.1204450159070.60389067697527.184758746520.403100190761.2938375094
103.489619175470.3723753101893.404172202552.119958991230.8538832860083.46833500098-0.211589526331.168544195890.431076554658-1.02798999786-0.06685042803710.350950738230.3299011827160.5756846461080.311123182370.627191940238-0.01386154102820.0007009687608560.7101739021210.06156131167340.55703069971834.223524299215.77676572554.0657022497
113.17832463124-0.437221146980.5266375564591.53432624467-0.260439447390.705500825873-0.0594564709313-0.792226550477-0.10344169010.032362393325-0.0233749646058-0.04396801679720.0197487466827-0.1740789826610.07245921161580.2974532966380.0247786519460.06258460979650.575442603172-0.0005212816310170.32573669790637.08962750782.0292115781974.7779153563
123.12541223128-3.046208073552.827985504289.22222526014-5.127140175874.33146737974-0.20082113453-0.963186676564-0.36192226671-0.3178066603110.393994451242-0.02860894216430.581344131508-0.46806496242-0.1339393577440.315065543015-0.01753858592840.04147844220410.7212522246710.1146208206060.42063584676751.1092081831-5.0451805929281.4510022209
132.48280549674-0.8786843035771.726630910492.02759463072-1.113540892612.396794891760.123226990808-0.949211378356-0.519060865477-0.1089508015540.2726221407910.2943187396760.493894302906-0.432786818069-0.396347172460.403093542304-0.00710830901370.003335893205930.8045296799240.2153637213110.49854660590945.1429589758-9.0078385085284.7358946102
142.295658647410.7436314414040.05605793752378.46103861578-3.781701318694.04529249202-0.06379225206-0.999292562613-0.5304553867920.476924553483-0.137499411156-0.4979567553690.144456911624-0.02281207920330.1421413548590.3951438097870.0741846525478-0.01683488633910.9650301424530.1848051343090.45243975077854.1134094397-7.4097796413190.9353738654
152.858989907420.964032041583-0.08305939302625.173487269311.06921116084.20279875888-0.0899311085566-0.0993036018442-0.2167121564290.2365972376970.07004137468750.08128194632530.29681806199-0.148168666170.014891010280.3789502413490.054965177882-0.02313738839450.340793463881-0.009128977676770.2368592534648.90578242435-2.2679360487730.5945551596
164.98498846273-0.314846992239-2.318257621034.441398678750.1042177107154.53085335848-0.0138498718434-0.119396439311-0.4958821085730.962599272016-0.0395625045289-0.5536758538320.3030916245250.538304995520.03996929164040.6629052525380.00836934717771-0.1789774258340.423176984262-0.0980417486090.61687204023921.4877765839-25.823777236513.9025168761
171.79285194714-0.235405925320.8527719193972.128838685720.4017082979265.2854703689-0.025394714-0.08376917070280.1096721772330.08837094774290.06787717611050.0326010823106-0.214036533052-0.0652511077441-0.03507182266190.3265701311990.0217267423092-0.04285429203970.376869350471-0.0105422581290.3383638705534.999034107095.0501232974811.7655447209
181.53528340646-1.42330479675-1.370169214943.983146263822.163673194191.55431333346-0.1742734414740.299622305274-0.4385519091710.3678683934140.0956024673848-0.1192999297550.3812747070830.1316726073260.03095713399880.4199258004320.0271431679974-0.0705103119430.506422838525-0.1880203138420.54832508644216.4005906079-24.89676011512.60932498829
191.12005667599-0.207501488721-0.5447196963069.60302569741-3.966572252252.69713051171-0.1022550539540.198145866301-0.2084178310210.3580813726520.07554750608440.694571974703-0.0886176274303-0.381396028631-0.002100973137360.4156203825450.0653738886054-0.02683951591810.592940941425-0.2817121929570.66164842647612.3869253167-27.2377820621-1.00924969966
202.32062861777-0.236070047819-0.7585975045576.15612950075-0.5376910940861.98727192428-0.07779156845060.432035029441-0.253842546130.289674542312-0.09081408318140.6387914972430.105848197789-0.3509265133310.1873389029720.3104188952530.036399764776-0.03788671400680.571554008882-0.2356153572740.53998497563111.2196938439-24.27443785681.3413124058
211.88083843575-1.314686862230.8253079412925.87734907051-1.350360711414.304485879760.05318318529720.36833720557-0.624685629161-0.215991024114-0.2001505965730.6714047559550.6424758820110.04310250440550.2021838940430.4856515471840.0203997774353-0.03334932861610.594509215056-0.313063241440.7782715665515.2361261982-36.6543688997-2.20972562878
222.715323636754.24802334047-3.458143662127.04407714363-4.849346671386.615497692950.3819596240540.2969240117930.0330246553563-0.0087820870916-0.01399640985980.787852783376-0.573030367741-0.895522598649-0.4113177419680.6874559718130.130556494993-0.07542607335440.612454149647-0.06489865339360.535207763576.711103846712.27198143348.348635027
239.198722155713.12257999044-1.603634506824.703749823390.1928037075328.816664950690.146484188417-0.114594155209-0.2062496518610.185350910537-0.208353547488-0.585807829054-0.9326880091080.3566113571260.09937999625520.6990119472440.059099569338-0.1020275490180.350262911157-0.01999881830830.40524345497417.088462427419.28815956537.1072259619
242.37379824831.914087186794.298552789193.852918086041.730863766479.63490656525-0.161128350685-0.1811507713510.134195403679-0.00486771826421-0.1407578445770.428289789404-1.00940120815-0.8926531262350.4936910071180.7704131708390.19848898058-0.07662342925260.580022939052-0.1919679537150.5258012581897.8905848683321.746520526845.7376205989
253.017058184160.403041058435-0.01682119208596.91281414572.899551890661.24841219953-0.928869113579-0.2514017804911.67407954206-0.3631970290040.0624419240143-0.965867592469-1.293503024890.2340885816480.7209793925731.197949568150.0683968372081-0.299188169620.47381575455-0.1424239653870.89888007271518.081516709931.572013138344.9159445999
266.292356774130.115654783837-1.858030577775.547850477585.976598707996.9748437094-0.09219226660870.05829356981460.8738106135440.1430917142560.3613199336250.317853561092-1.79672815574-0.211072380325-0.08013606404931.117777924060.238872272814-0.06977047455640.499718108718-0.03871712656720.5917542946856.5938468941926.470284343238.5308307975
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'C' and (resid 1 through 17 )CA1 - 171 - 17
22chain 'C' and (resid 18 through 60 )CA18 - 6018 - 60
33chain 'C' and (resid 61 through 83 )CA61 - 8361 - 83
44chain 'C' and (resid 84 through 122 )CA84 - 12284 - 122
55chain 'C' and (resid 123 through 156 )CA123 - 156123 - 156
66chain 'C' and (resid 157 through 225 )CA157 - 225157 - 225
77chain 'D' and (resid 4 through 31 )DC4 - 311 - 28
88chain 'D' and (resid 32 through 48 )DC32 - 4829 - 45
99chain 'D' and (resid 49 through 61 )DC49 - 6146 - 58
1010chain 'D' and (resid 62 through 75 )DC62 - 7559 - 72
1111chain 'D' and (resid 76 through 141 )DC76 - 14173 - 138
1212chain 'D' and (resid 142 through 152 )DC142 - 152139 - 149
1313chain 'D' and (resid 153 through 190 )DC153 - 190150 - 187
1414chain 'D' and (resid 191 through 215 )DC191 - 215188 - 212
1515chain 'A' and (resid 1 through 121 )AD1 - 1211 - 121
1616chain 'A' and (resid 122 through 226 )AD122 - 226122 - 222
1717chain 'B' and (resid 1 through 101 )BH1 - 1011 - 101
1818chain 'B' and (resid 102 through 128 )BH102 - 128102 - 128
1919chain 'B' and (resid 129 through 150 )BH129 - 150129 - 150
2020chain 'B' and (resid 151 through 174 )BH151 - 174151 - 174
2121chain 'B' and (resid 175 through 214 )BH175 - 214175 - 214
2222chain 'E' and (resid 30 through 42 )EK30 - 421 - 13
2323chain 'E' and (resid 43 through 98 )EK43 - 9814 - 41
2424chain 'E' and (resid 99 through 116 )EK99 - 11642 - 59
2525chain 'E' and (resid 117 through 134 )EK117 - 13460 - 77
2626chain 'E' and (resid 135 through 151 )EK135 - 15178 - 94

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