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- PDB-7ttz: Heterodimeric IgA Fc in complex with Staphylococcus aureus protei... -

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Basic information

Entry
Database: PDB / ID: 7ttz
TitleHeterodimeric IgA Fc in complex with Staphylococcus aureus protein SSL7
Components
  • (IgA Fc) x 2
  • Superantigen-like protein SSL7
KeywordsIMMUNE SYSTEM / IgA / heterodimer / antibody Fc / antibody engineering
Function / homology
Function and homology information


Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type ...Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Chem-1PG / Uncharacterized protein DKFZp686L19235
Similarity search - Component
Biological speciesHomo sapiens (human)
Staphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsBoulanger, M.J. / Verstraete, M. / Heinkel, F. / Escobar, E. / Dixit, S. / Von Kreudenstein, T.S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Mabs / Year: 2022
Title: Engineering a pure and stable heterodimeric IgA for the development of multispecific therapeutics.
Authors: Heinkel, F. / Verstraete, M.M. / Cao, S. / Li, J. / Farber, P. / Stangle, E. / Silva-Moreno, B. / Peng, F. / Dixit, S. / Boulanger, M.J. / Spreter Von Kreudenstein, T. / Escobar-Cabrera, E.
History
DepositionFeb 2, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IgA Fc
B: IgA Fc
C: Superantigen-like protein SSL7
D: Superantigen-like protein SSL7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,21318
Polymers93,7934
Non-polymers2,42014
Water2,918162
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)135.505, 165.447, 46.434
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

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Protein , 3 types, 4 molecules ABCD

#1: Protein IgA Fc


Mass: 23965.229 Da / Num. of mol.: 1 / Mutation: A412F, T414Y, N337T, I338L, T339S, C311S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: Q6MZV6
#2: Protein IgA Fc


Mass: 23727.930 Da / Num. of mol.: 1 / Mutation: L396V, W398T, I416L, N337T, I338L, T339S, C311S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: Q6MZV6
#3: Protein Superantigen-like protein SSL7


Mass: 23050.020 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Escherichia coli (E. coli)

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Sugars , 1 types, 1 molecules

#4: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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, 175 molecules

#5: Chemical
ChemComp-1PG / 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL


Mass: 252.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C11H24O6 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.77 Å3/Da / Density % sol: 55.67 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 30% PEG MME 550, 0.1 M HEPES pH 7.5, 0.2 Magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→39.56 Å / Num. obs: 48763 / % possible obs: 98.6 % / Redundancy: 2 % / Biso Wilson estimate: 48.67 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.12 / Net I/σ(I): 14.8
Reflection shellResolution: 2.35→2.43 Å / Rmerge(I) obs: 1.508 / Mean I/σ(I) obs: 2.15 / Num. unique obs: 3864 / CC1/2: 0.639

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Processing

Software
NameVersionClassification
Blu-Icedata collection
XDSdata reduction
XDSdata scaling
PHENIX1.18.2_3874phasing
PHENIX1.18.2_3874model building
PHENIX1.18.2_3874refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2qej
Resolution: 2.35→39.56 Å / SU ML: 0.3361 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.5809
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2475 3756 4.54 %
Rwork0.2003 78988 -
obs0.2025 43760 98.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.07 Å2
Refinement stepCycle: LAST / Resolution: 2.35→39.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6237 0 113 162 6512
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00826455
X-RAY DIFFRACTIONf_angle_d1.01378685
X-RAY DIFFRACTIONf_chiral_restr0.0495976
X-RAY DIFFRACTIONf_plane_restr0.00671109
X-RAY DIFFRACTIONf_dihedral_angle_d13.9352905
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.380.40031160.30222459X-RAY DIFFRACTION83.36
2.38-2.410.35641240.29332724X-RAY DIFFRACTION92.2
2.41-2.440.31781390.28562876X-RAY DIFFRACTION94.84
2.44-2.480.34651360.28322922X-RAY DIFFRACTION99.74
2.48-2.510.331400.26812972X-RAY DIFFRACTION99.97
2.51-2.550.3471420.26532989X-RAY DIFFRACTION100
2.55-2.60.24361420.26242932X-RAY DIFFRACTION98.46
2.6-2.640.3111390.25572961X-RAY DIFFRACTION100
2.64-2.690.3381440.26542961X-RAY DIFFRACTION99.78
2.69-2.740.30951430.2483008X-RAY DIFFRACTION98.81
2.74-2.80.32171360.25062894X-RAY DIFFRACTION99.57
2.8-2.860.32491420.24642930X-RAY DIFFRACTION98.49
2.86-2.920.26691420.2452987X-RAY DIFFRACTION99.14
2.92-30.32211380.23812921X-RAY DIFFRACTION99.74
3-3.080.30161480.23282997X-RAY DIFFRACTION100
3.08-3.170.23021380.2222921X-RAY DIFFRACTION99.61
3.17-3.270.26071450.20613006X-RAY DIFFRACTION99.97
3.27-3.390.27781420.22222942X-RAY DIFFRACTION99.61
3.39-3.520.28761390.21842927X-RAY DIFFRACTION98.11
3.52-3.680.24091410.19142954X-RAY DIFFRACTION99.55
3.68-3.880.21371420.17983005X-RAY DIFFRACTION99.02
3.88-4.120.20821390.1682932X-RAY DIFFRACTION99.97
4.12-4.440.18911430.15122950X-RAY DIFFRACTION99.9
4.44-4.880.18941400.14882937X-RAY DIFFRACTION98.5
4.88-5.590.22051480.15752964X-RAY DIFFRACTION100
5.59-7.030.20991340.19872956X-RAY DIFFRACTION99.01
7.04-39.560.22991340.1832961X-RAY DIFFRACTION99.07
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)
16.295606143964.76054456987-3.90224079384.89091163259-5.678871605257.59397250150.298501214488-0.0190243819420.9968711412170.440260515756-0.282008103280.372899492962-0.815307340370.363021464479-0.06362879062420.597385829551-0.08047388131930.09226010731670.519400926151-0.09819352487710.747274663003-3.3215518499258.096705035215.830177998
23.442965009281.81742000133-3.366976726015.46531648486-2.005427040093.28372331941.38513132436-0.9764383782181.602876471770.0142350613679-0.35624952057-0.499909392044-1.492509695920.278222129391-0.9258964775730.764583003135-0.05902627364060.211542679880.714532514775-0.09238095747291.13129506507-5.5170146089370.557844207418.4996785049
37.302297628345.53112582693-1.668081690076.22709928215-1.469132922594.262416453410.47870418011-0.447552029991.086405449720.357772595258-0.3125011212041.10190681498-0.7795355713920.273332416759-0.122150673030.8989929676980.09031369867110.1646274738760.451770512785-0.05331325914270.791999721424-4.6643681971764.862732559815.262732236
45.46355249582-3.445982498390.04471989781965.21805043804-0.008311452522251.52431398007-0.0644129028-0.07501283453280.103751588139-0.107784960448-0.0262215626992-0.04066691124550.1616574418860.009113692311990.09129774228980.348886725924-0.05101540197380.03522280370710.391792411481-0.02521009052260.26543174958-1.0900551254431.498469945413.3007658265
51.960964158950.5356918163860.4991631159197.683360090463.295717468912.69955058995-0.0374450929779-0.0815307450402-0.00134571761564-0.181330756232-0.0340668010458-0.164298386133-0.3046521558970.006525680621580.02455027495930.40533455158-0.136470517449-0.03387097688310.4644783220240.08211150964790.33080439555925.107770148854.2889418021-3.33094859065
68.90086602957-4.84199688027-1.944962464144.997398558444.051127613114.023750608150.177574773740.70536083493-0.442786658106-0.513073258901-0.6869417260240.37984555658-0.698407840005-0.6453373859410.6621822863010.507920269582-0.1236681742230.03176413016710.6469118543350.01409208124040.49314686005923.301485053459.8899207581-6.31763384249
72.71875781123.41377348112-1.111326966447.43319722614-0.9826208638061.5703167998-0.0402237574588-0.0393802664619-0.3072533907050.0614702563979-0.082744547534-1.12094844067-0.2382274677260.3729230113320.1325677835920.297960854082-0.0458272367401-0.05557801428950.4774812985150.01477361704030.36126069049428.473196975446.40623220430.149109003593
88.652194282031.015097693341.150063635673.167752682230.3447810086332.932847597120.05763019576390.217041232315-0.04822960364160.0547599405236-0.07811810342850.2224749235710.218671969191-0.4317021600060.02323431745030.341708679936-0.02707026571420.04654823214880.315513543792-0.00845133164020.2145774567686.7907267207728.6090056274-0.960599312221
97.343481941121.46154221282-2.364998995337.43481847475-1.404881672888.07660950543-0.221204668969-0.476576782189-0.0728198506770.953907188861-0.4494012258410.578024319461-0.00241759980319-0.4294484551770.6227959248830.7346337801560.06044814657850.1469526242620.421389881036-0.08478788203430.57329827343413.605301401710.9393471132-2.95952992247
103.516209211840.1908509386610.1337610941465.784672349540.3520533566318.47729039564-0.06684289973290.4465136093480.185811738709-0.5843899819580.0799904571865-0.207329766760.1813079583610.459098449894-0.0511875151690.349820114871-0.007263523933110.09167770817430.4355413702940.04412977000270.34281717255927.592986535923.9068522116-18.0527717588
118.773930190883.20548453135-1.04502430617.082593854683.963125698248.005363586850.2202421002990.0196702534138-0.333330279146-0.4092641465470.184665323893-1.336222847710.4554420292641.2918591421-0.4890652537990.5130915789770.1987288049610.07371226208290.6520489117950.02889109268190.67048910103236.777905654320.616498847-14.2337313824
125.043428938-3.606138770831.342259680818.931857516860.5847678500052.83876859060.3600081766650.2566647475660.287614280326-0.221052272839-0.362243141392-0.7055997679290.3365153940230.1892902349470.01417584929420.381170006053-0.03740631724560.05836429609710.4039485535470.04719954979830.34002255171726.344706440919.3407798628-16.0834475675
134.229707142732.5461273406-5.441157336974.55038556076-3.553930039479.891262845540.03225952254980.01095920915830.00636286294952-0.0733921006498-0.03700464326420.4688013670620.337393881290.09396767885980.1308288459460.838315094330.05619872901270.05342885776620.461376261187-0.05231746326590.57903063081124.2386389103-5.32996361759-10.5773314275
143.542231381595.69788453913-1.17274880899.20240320325-1.738120216282.938284687090.0734045999190.733437869084-0.4316171157690.2318943120220.146892386168-0.1986949786690.7093624145080.166209144784-0.1645309321180.6864024976560.05944220619020.0420161315420.40177473308-0.05566758525240.37676183922824.0470321164.74761020525-11.4701040672
159.01570034637-0.475896559372-2.740944266636.1463195254-0.1720366761112.9215326135-0.224697902935-0.435351783689-0.6251427548470.6830908436740.07143474864650.05154877757230.4561806945720.007152769453380.1729218282780.9901903006930.01275954773390.07793523546990.3302734393670.04063830771820.44862030013919.88365716832.06713542248-1.60369508568
168.44531059798-5.81674665306-0.3916881998878.962299436391.323619842172.80458475138-0.306491850444-1.5358136024-0.7235393315711.041397674140.238543854439-1.438953302340.3336335837070.3770633336870.1117164133530.9123189101810.207763523235-0.2017773454090.5922609607980.09837977771370.88727776806535.8489754041.18832075756-2.49070415515
174.562558273652.671684916752.038584896918.29680916616-1.225134918795.265352823580.0973829104305-0.00817895697288-0.3572244739230.696555629959-0.415015666245-0.5888482512620.2772214341250.1544478192580.30392948980.677081824730.1127443364320.08126385218690.4466130826330.006454429736990.3723372570529.31557013784.81326990209-4.87644575292
184.23932697795-2.79055752752-2.974142218586.943773770385.337787103424.11525334505-0.281479187528-0.477598601001-0.1109955141630.03275510601470.498013914201-0.201378148827-0.03813798331940.406378771191-0.1776069460530.2952710693010.06147146752430.01800038911110.4928653417070.0631932875260.36019736452-18.540026001823.327515054922.1345628365
195.541254727151.06086965182-2.070304510886.21700169207-2.347635281117.448377098950.0196610571673-0.1824597985060.6930367477390.3230419945880.2179521357910.262827608163-0.572826954984-0.592347849193-0.2630106464780.4042211518760.08437810839170.0484627207650.484594965796-0.1267281585490.435227032885-22.359539099139.682558202627.8937100835
208.730385823993.22042375578-0.1745588538232.3148792209-1.658149081082.37772162389-0.0713642328124-0.4147423413280.117942753353-0.2753014638640.03344961800370.1111480866260.0194719520549-0.09036107651830.07259126963540.4447728151230.04954783058260.00477800180190.466916507665-0.09150347308070.255957710224-19.184868382633.658695947829.0914580635
218.967053101611.26307890457-5.036839491613.25167751582-0.4245554056035.333339975630.364767854961-0.3033406466580.747552031850.6290539059470.202232498033-0.0152983545082-0.184859357743-0.237189588978-0.5666307153210.3737638378580.089557167207-0.005799838963740.559239260106-0.02019695584020.348270074028-36.41799194229.011317269135.192773402
225.29615208376-1.23046215341-1.854225862553.807226598415.414340387537.67113291956-0.00590772064145-0.323614926018-0.0695799614104-0.1065661983190.461215645797-0.2395955751670.466516941677-0.394752157915-0.4602716596170.7375989011110.1017471309150.02244393192130.4025591550780.1104759933710.40595797988-34.311254441712.386406354325.9067210283
235.08301164466-0.342238763405-3.206097927426.655808747982.903698644667.7214726395-0.169549637326-0.307533674442-0.05469851220480.2084939134430.267618520675-0.4442209654290.4187457188840.652939249077-0.0589301077210.2551567666860.0972088047458-0.01279349653230.3791766608130.04546164515080.294727529045-24.45596825816.321453184821.5708295624
243.30704099229-0.502164738948-4.564090831891.843581816051.313549764516.497719317760.1330563618221.047135874710.149531736713-0.609147452699-0.08417024053140.0811437042712-0.343632351565-0.3849612210290.01502520819360.5413463936560.08582413949780.009331226766310.4634881280650.05796562268340.370010066835-36.0051289719.114230953814.9949366103
254.784273010783.282659683880.422804347015.17599892248-0.002258715156334.85697681896-0.116991698204-0.002364903913170.157354301501-0.4257163863230.2281123875760.01156539716460.116100035405-0.00706047220498-0.108414076070.3732639738610.095782187448-0.02707457564580.3935987189440.0223637358680.261455085594-31.266171094621.126284656818.0171350656
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 242 through 271 )AA242 - 2711 - 30
22chain 'A' and (resid 272 through 288 )AA272 - 28831 - 45
33chain 'A' and (resid 289 through 339 )AA289 - 33946 - 96
44chain 'A' and (resid 340 through 450 )AA340 - 45097 - 207
55chain 'B' and (resid 242 through 282 )BC242 - 2821 - 41
66chain 'B' and (resid 283 through 303 )BC283 - 30342 - 62
77chain 'B' and (resid 304 through 352 )BC304 - 35263 - 111
88chain 'B' and (resid 353 through 451 )BC353 - 451112 - 210
99chain 'C' and (resid 9 through 21 )CD9 - 211 - 13
1010chain 'C' and (resid 22 through 55 )CD22 - 5514 - 47
1111chain 'C' and (resid 56 through 75 )CD56 - 7548 - 67
1212chain 'C' and (resid 76 through 101 )CD76 - 10168 - 90
1313chain 'C' and (resid 102 through 128 )CD102 - 12891 - 117
1414chain 'C' and (resid 129 through 147 )CD129 - 147118 - 136
1515chain 'C' and (resid 148 through 162 )CD148 - 162137 - 151
1616chain 'C' and (resid 163 through 172 )CD163 - 172152 - 161
1717chain 'C' and (resid 173 through 201 )CD173 - 201162 - 190
1818chain 'D' and (resid 7 through 33 )DE7 - 331 - 27
1919chain 'D' and (resid 34 through 66 )DE34 - 6628 - 60
2020chain 'D' and (resid 67 through 89 )DE67 - 8961 - 83
2121chain 'D' and (resid 90 through 101 )DE90 - 10184 - 95
2222chain 'D' and (resid 102 through 128 )DE102 - 12896 - 115
2323chain 'D' and (resid 129 through 155 )DE129 - 155116 - 142
2424chain 'D' and (resid 156 through 172 )DE156 - 172143 - 159
2525chain 'D' and (resid 173 through 201 )DE173 - 201160 - 188

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