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- PDB-7q4g: Structure of coproheme decarboxylase from Corynebacterium dipthth... -

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Basic information

Entry
Database: PDB / ID: 7q4g
TitleStructure of coproheme decarboxylase from Corynebacterium dipththeriae Y135A mutant in complex with coproheme
ComponentsCoproheme decarboxylase from Corynebacterium diphtheriae Y135A mutant in complex with coproheme
KeywordsBIOSYNTHETIC PROTEIN / coproheme decarboxylase / coproporphyrin dependent heme b biosynthesis / porphyrin binding alpha-beta barrel protein
Function / homologyHeme-dependent peroxidase ChdC/CLD / Chlorite dismutase / Dimeric alpha-beta barrel / oxidoreductase activity / heme binding / Chem-FEC / DI(HYDROXYETHYL)ETHER / Uncharacterized protein
Function and homology information
Biological speciesCorynebacterium diphtheriae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsMichlits, H. / Valente, N. / Mlynek, G. / Hofbauer, S.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundP29099 Austria
CitationJournal: Front Bioeng Biotechnol / Year: 2021
Title: Initial Steps to Engineer Coproheme Decarboxylase to Obtain Stereospecific Monovinyl, Monopropionyl Deuterohemes.
Authors: Michlits, H. / Valente, N. / Mlynek, G. / Hofbauer, S.
History
DepositionOct 30, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 23, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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

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Assembly

Deposited unit
A: Coproheme decarboxylase from Corynebacterium diphtheriae Y135A mutant in complex with coproheme
B: Coproheme decarboxylase from Corynebacterium diphtheriae Y135A mutant in complex with coproheme
C: Coproheme decarboxylase from Corynebacterium diphtheriae Y135A mutant in complex with coproheme
D: Coproheme decarboxylase from Corynebacterium diphtheriae Y135A mutant in complex with coproheme
E: Coproheme decarboxylase from Corynebacterium diphtheriae Y135A mutant in complex with coproheme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,63311
Polymers135,9845
Non-polymers3,6496
Water15,151841
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21550 Å2
ΔGint-158 kcal/mol
Surface area41330 Å2
Unit cell
Length a, b, c (Å)61.117, 123.517, 78.300
Angle α, β, γ (deg.)90.000, 98.020, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Coproheme decarboxylase from Corynebacterium diphtheriae Y135A mutant in complex with coproheme


Mass: 27196.865 Da / Num. of mol.: 5 / Mutation: Y135A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium diphtheriae (bacteria) / Gene: BT093_04375 / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner / References: UniProt: A0A2T1BSE4
#2: Chemical
ChemComp-FEC / 1,3,5,8-TETRAMETHYL-PORPHINE-2,4,6,7-TETRAPROPIONIC ACID FERROUS COMPLEX / FE-COPROPORPHYRIN III


Mass: 708.538 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C36H36FeN4O8 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 841 / Source method: isolated from a natural source / Formula: H2O
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: 2.19 Å3/Da / Density % sol: 43.83 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, MgCl2, Sodium Phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0723 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 23, 2018 / Details: Toroidal mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0723 Å / Relative weight: 1
ReflectionResolution: 1.82→48.31 Å / Num. obs: 659722 / % possible obs: 97.65 % / Redundancy: 6.6 % / Biso Wilson estimate: 27.41 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.1912 / Rpim(I) all: 0.0796 / Rrim(I) all: 0.2074 / Net I/σ(I): 5.73
Reflection shellResolution: 1.82→1.885 Å / Redundancy: 4.6 % / Num. unique obs: 8371 / CC1/2: 0.221 / Rpim(I) all: 0.9429 / Rrim(I) all: 2.079 / % possible all: 81.68

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Processing

Software
NameVersionClassification
PHENIXdev_4380refinement
XDSdata reduction
PDB-REDOrefinement
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6XUC
Resolution: 1.82→48.31 Å / SU ML: 0.2659 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.0619
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2194 2100 2.09 %
Rwork0.1729 98377 -
obs0.1739 100477 97.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.54 Å2
Refinement stepCycle: LAST / Resolution: 1.82→48.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9334 0 252 841 10427
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01539954
X-RAY DIFFRACTIONf_angle_d1.04713568
X-RAY DIFFRACTIONf_chiral_restr0.11181358
X-RAY DIFFRACTIONf_plane_restr0.01271764
X-RAY DIFFRACTIONf_dihedral_angle_d9.56891383
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.880.38211100.37648240X-RAY DIFFRACTION80.21
1.86-1.910.36711260.32755924X-RAY DIFFRACTION88.03
1.91-1.960.32741400.28446540X-RAY DIFFRACTION97.56
1.96-2.020.27541420.24456666X-RAY DIFFRACTION99.94
2.02-2.080.27031440.22456714X-RAY DIFFRACTION99.99
2.08-2.160.26521430.2116732X-RAY DIFFRACTION99.96
2.16-2.240.24791440.20576716X-RAY DIFFRACTION99.91
2.24-2.340.22361430.18896703X-RAY DIFFRACTION99.93
2.34-2.470.25641440.17646724X-RAY DIFFRACTION99.93
2.47-2.620.23961430.17286727X-RAY DIFFRACTION99.97
2.62-2.820.22261440.16586713X-RAY DIFFRACTION99.99
2.82-3.110.22271430.16136738X-RAY DIFFRACTION99.99
3.11-3.560.19561430.14516752X-RAY DIFFRACTION99.97
3.56-4.480.15591440.12596741X-RAY DIFFRACTION99.97
4.48-48.310.19831470.15626837X-RAY DIFFRACTION99.86
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)
15.053006803320.1477356849111.928154900011.944212988380.5645563365282.76550007022-0.05596775459170.04455701117120.209993323456-0.137458054847-0.042393331282-0.03753243473930.01447209968810.05158766652180.1274305065620.1886354317390.01161862372540.07583903409230.171450799510.01885393923580.177037023319-7.7012917305218.3841403683-43.6596374389
22.830416654880.5346795230160.5865566591951.899169509540.08200328967390.256509087985-0.06570871632070.503880208228-0.189297589066-0.2154543947640.0549525253676-0.3288910489310.06021344349080.3787190269220.001540260193890.201505750554-0.01322877906640.06898561870650.3632172444280.0139942150220.247989287683-0.9903573461218.9831966333-43.6845807177
32.187248829380.07507594528530.04401393851761.61444917299-0.02278532217671.153567980360.007530559508080.152314903196-0.117829133169-0.1630453572620.0162722096968-0.007350289949780.01803337198340.0942827149458-0.02228187088960.188422687177-0.01750648420350.02795664733630.216771479862-0.01123717310760.172214280738-14.310890867119.2492608736-42.2664401557
44.764748174216.20849314536-1.240553226438.20663915214-1.427009439985.292823914880.01276972391110.689632577560.92786172893-0.3638070254580.1480701983080.819915459612-0.233513750957-0.322280366675-0.2000980954390.1951530537110.0282196609244-0.03261803404090.3141786833180.07041430173440.340990844563-31.111559142934.0457437192-44.6834059959
50.680862487301-0.146841558840.09649130119891.60420233723-0.1368058447760.907392448392-0.003091535093280.1730342451990.0577521827655-0.106492507479-0.0389624626913-0.0915588025972-0.1278624143780.1450776249650.03361370217920.136349120371-0.02132324652060.01148244092030.1962279223030.01947559186220.183699875073-14.017447722729.3352193548-38.7871956463
65.914932528312.37451317095-0.3287967832794.8356608347-0.02721203009312.74296497830.1770704655550.2824842640430.2651604612590.232692947407-0.1025433909760.3733572098720.340294352875-0.050575164586-0.07576136998820.3766888520580.08540658329030.02535175462040.1815371961510.001255583366370.185184238931-17.8032094461-5.33593681985-27.9382553001
72.93656193424-0.06106717461420.05387032890742.88059800368-0.4216213177352.39539631188-0.03299962294070.141328886698-0.625570719250.049144631504-0.0830222842348-0.307902275810.6663349483370.3264132782570.07973022576660.3543307415450.08229626407810.03365580530750.223597595274-0.05315100307830.321215741491-11.623850429-7.080494061-30.2299130764
81.61069918882-0.465741919745-0.5975599195391.331930147580.1436963249181.5636306092-0.02242549280740.049261971813-0.2668148574320.0495797961938-0.01774554408070.1211874908850.345684570178-0.0812944295440.03513222123040.292444240758-0.01575273955290.01514852646860.18242844813-0.01227032399540.289859842549-23.3877187166-1.82809389012-26.2253731912
94.617400434770.984333235012-4.67343771133.74320102996-1.086494382874.7315099797-0.24123648340.351912090833-0.580344008937-0.0436154064695-0.1174565421411.051863806750.352047657616-1.115508411820.4042184579930.231840159674-0.0487377774448-0.01197581443090.359925999081-0.009279868416260.481898659537-43.69722232097.58437676722-32.7872369338
100.3207176937090.0987090880847-0.2673013707512.054055984891.214048128739.83231700109-0.01148437787910.0248421744477-0.159967763424-0.0748111997870.07371585753550.1150128811470.269163448842-0.16895955631-0.05483331750260.187418403848-0.0342351495678-0.005879296259580.188990927156-0.01397192666650.30129147652-28.180127142.13169615234-32.9503727108
115.25702598641-5.26639707484-2.943083585697.589540072352.894370268074.30876865384-0.2462075591190.316392742792-0.6294800361060.0518896865009-0.05859194837470.6219509542450.294878962913-0.3178209589490.2700793592730.166245537905-0.0553177872035-0.02130126229440.19121779568-0.02150653769050.237047929737-27.621810225710.1711987013-42.1496875897
123.42305710352-0.3949419442260.09220456704841.92019243437-0.2266156296262.23378169452-0.09133297700230.172631841178-0.37682066703-0.07191719361150.02135410903030.001831482222750.3335906759580.2833836848390.07615067673340.1807048976480.00233668372650.0172534648460.161827158214-0.01089533299060.180022632553-18.7555153385.63364300973-33.9013039821
134.47043102456-2.622894593362.338564421944.54661049167-1.77083858274.57407211566-0.191292262962-0.01243391147880.2292751307260.3782177594960.113658320133-0.227752919269-0.3257767337230.2931909452370.1212930186970.221148963287-0.08376133282430.01430081227270.253437284089-0.01723072279790.261761977266-0.83129238389841.174085387-23.9819655978
144.3703512936-1.18145396835-0.6108011488340.953567820291.316385854372.193326281880.03451128960390.2007261661650.4086289779810.04162524785330.00425763895761-0.686278540174-0.439009693920.626460408245-0.03513134375290.282908060385-0.139279187591-0.09024983639020.4003688636640.06659537764870.5012223726449.9777352895741.3291864511-22.1919975111
151.16200234855-0.2006574344320.07948384148671.29059767723-0.3254404065181.29082247043-0.01188568342460.09801157250340.2003541129130.114620317192-0.0550842253458-0.196301873339-0.2574528369630.2168134246630.07049687603780.221507810761-0.0446397822238-0.0140847644550.1857912917830.0182508218820.258388600268-6.5124979606439.7739843018-23.9927171777
169.792567498073.848336666776.062336299795.677699555133.80031207814.29534993601-0.251565495543-0.2371784796620.670449560140.205272831484-0.06667416676970.374585505046-0.775809940709-0.5799165185220.4121472660530.4141155142260.07949396719040.04432014352410.2101645780110.03764403596270.338343328646-28.191846150450.3928215148-22.1116652474
171.44283226142.20179787650.828345518096.13420419524.589660245657.394799029690.09601544580150.009042063104850.100534901530.228468623869-0.095860960873-0.0193115252568-0.341747953807-0.00214780217871-0.01074510056550.2162821377550.0125499140005-0.007550819416860.1641393201650.05007234874620.255085952055-12.966800540944.8716033292-19.6758079048
184.568182080811.010353177491.716126785141.70219036596-1.488686183723.14860500808-0.1665978375920.04092886335090.153191113598-0.04510336476250.0909714872376-0.0499507652509-0.7710830268010.08046931147970.05727716002240.434085501112-0.01260102143790.001151170503750.165563879861-0.03873291681830.287577447265-16.965532998245.3227329845-8.022745642
197.29634778217-1.021773208860.6403330625321.5834494689-0.3615795501281.46184924079-0.05675780927290.0562347797522-0.02776667006330.05045852094870.0152903765068-0.0116019563721-0.0878754949238-0.01435548145860.02637745904590.2349135895470.006384585121950.02360015227990.165300852140.01357616939450.2061227598-19.387093432938.1929616492-15.9840494153
205.37979647384-3.191212213411.511122262535.17007666547-1.07596320671.63379526345-0.2659671579160.1368239860360.5539853892551.067954412020.128949887112-1.27433101547-0.4220351223350.8657484942530.1632696969850.412840121792-0.0815988738567-0.1610853859010.458538099769-0.03214894241380.4965105684638.5083258001938.1015019053-11.0889619037
212.87879019293-0.776692576899-0.2560208356445.169628698980.371845180022.2999943092-0.115635118153-0.2322539527410.3357630223580.09212071311980.22445105983-0.734123606938-0.1892731764040.307909748177-0.08618597400350.2179420515620.00472518862333-0.02381415927430.226669398151-0.03794556990620.253570147146-3.1989955671628.75827745375.00617898872
222.02807413778-1.154530313280.975716072912.09235488808-0.3434077890331.18056281285-0.0944668793867-0.2479014289790.249031516530.07269862661320.0948595077811-0.123762498376-0.158587301178-0.133154597641-0.003570688635570.297419567938-0.003246650884570.02985201082630.213990241667-0.03347422125690.227658301973-17.507772033932.82648763431.6335039272
233.64200555332-2.073148728932.276329178057.33028737782-3.475258856222.93392620433-0.271058347663-0.5148520250380.1711772549750.5405643009540.3662356334790.556691863748-0.892978689326-0.721548579162-0.1474045754940.3705516487290.1238124594620.02502452323610.368992453958-0.09147340541670.326848734882-34.994057571534.77754955824.40001897223
241.722886602340.04902786138620.2826849734470.6052047233240.05083584256131.65715700473-0.0695270229367-0.1969400614840.01746122359420.1673228178880.0384936130606-0.0224996577780.0261139208328-0.02979971089740.02662065985940.2640306734710.01988217554270.03085613699720.173638143547-0.01181836333380.185807467426-19.488137518724.6673289483.46422570991
252.566994830870.2607629140921.933707517414.40860970308-0.2105995170981.61923033712-0.031779294143-0.487601869795-0.08620444562780.7010047195740.06586358473180.4434366729050.332826129788-0.510440967684-0.05407790742470.392098711166-0.01681819656170.01210028208760.2932634897750.04604823585020.247742646456-22.65298256014.858625536885.20901312
262.57830863262-1.031229439651.749005690796.60487670471-1.520805978284.920478168070.1108928532310.0275381778276-0.64898672070.317628806474-0.056582489448-0.274986316430.7162191610750.53220276965-0.04258749649180.3794677130630.10579065628-0.07824145882460.276581022344-0.009989331404330.406474433091-3.37033191769-6.11715016922-0.145395679603
271.69879188882-0.04779976024970.6787666055862.090008964391.095415152172.15389899452-0.0171990077119-0.197756548222-0.260032341770.4265572155890.0883806760732-0.09340678127620.3893457787160.0723948587159-0.05648437368390.3379335778290.03349029164810.01114647587780.1758647087710.05538610208110.247902427037-12.53923388613.067872732940.205988866192
280.410017148746-0.04083156253990.8246746233180.177105825141-0.08331496457021.68590005671-0.177676631981-0.2062051889670.0718198118665-0.0759513587111-0.08361182281220.8925885038230.0158931572286-0.5373174980960.2940886058430.593133447236-0.1306682300220.1132279337910.4294797495240.03051116126670.721040843798-33.14780803912.127303626654.71504690463
292.71473201733-2.075561742240.1955449642876.970968138510.426750001642.450158473290.037796770775-0.177263961395-0.0105917430946-0.02531341427620.02152442524690.35153881540.0233401403168-0.270724734869-0.05880750874020.208363333277-0.04488431833790.03950943114960.1810096360840.008629775630020.198172422748-32.474379829412.5795682563-6.74102695042
304.65189628129-1.97971181951-1.742948309414.7701464934.916869219845.09481990083-0.10804339609-0.225289454341-0.2323072376660.417526552278-0.2954378815461.512199632750.143727329427-0.869440482160.479909122980.2866299421120.01818021830730.1042935988940.4617437970310.06856525325840.469979685463-44.97115505559.95579784266-4.57173996887
318.170367438567.651964636876.953615345148.747789493477.218653789438.08198365937-0.0778544649943-0.4593864556590.05527456090190.122722487685-0.2227407518080.5941680338690.338803566884-0.8406858757970.2310429560820.363939259583-0.04618428350110.1117298791150.3594643474460.05703201644820.382012821729-35.2758959806-1.58884318713-4.31302623986
321.585490148860.7118443182851.258697349271.438125947840.2554596310752.79008726840.0735223595055-0.119069463816-0.1062373602880.112964156128-0.06027372348050.03645498319840.245669043145-0.195464163019-0.001234779169180.184422280667-0.01599721304120.06964250496210.1714414020990.007906785376210.219257324086-31.30230468516.30505264521-9.70011375998
337.27519797242-2.263849908560.07880931638795.068643036810.03360895034142.670071058820.0216410051444-0.0816149925305-0.8986317408220.21339088295-0.00766763606439-0.2693151157460.7757557079940.310702266638-0.01026245913990.4315777407560.0563890667764-0.01628151118670.211193690535-0.01022867709750.360501495674-12.9280621338-6.86119751292-8.00289299465
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 6 through 33 )AA6 - 331 - 28
22chain 'A' and (resid 34 through 78 )AA34 - 7829 - 73
33chain 'A' and (resid 79 through 147 )AA79 - 14774 - 142
44chain 'A' and (resid 148 through 165 )AA148 - 165143 - 160
55chain 'A' and (resid 166 through 235 )AA166 - 235161 - 230
66chain 'B' and (resid 6 through 33 )BC6 - 331 - 28
77chain 'B' and (resid 34 through 78 )BC34 - 7829 - 73
88chain 'B' and (resid 79 through 147 )BC79 - 14774 - 142
99chain 'B' and (resid 148 through 162 )BC148 - 162143 - 157
1010chain 'B' and (resid 163 through 191 )BC163 - 191158 - 186
1111chain 'B' and (resid 192 through 203 )BC192 - 203187 - 198
1212chain 'B' and (resid 204 through 235 )BC204 - 235199 - 230
1313chain 'C' and (resid 5 through 33 )CE5 - 331 - 29
1414chain 'C' and (resid 34 through 60 )CE34 - 6030 - 56
1515chain 'C' and (resid 61 through 147 )CE61 - 14757 - 143
1616chain 'C' and (resid 148 through 162 )CE148 - 162144 - 158
1717chain 'C' and (resid 163 through 191 )CE163 - 191159 - 187
1818chain 'C' and (resid 192 through 203 )CE192 - 203188 - 199
1919chain 'C' and (resid 204 through 221 )CE204 - 221200 - 217
2020chain 'C' and (resid 222 through 235 )CE222 - 235218 - 231
2121chain 'D' and (resid 6 through 92 )DH6 - 921 - 87
2222chain 'D' and (resid 93 through 147 )DH93 - 14788 - 142
2323chain 'D' and (resid 148 through 165 )DH148 - 165143 - 160
2424chain 'D' and (resid 166 through 235 )DH166 - 235161 - 230
2525chain 'E' and (resid 8 through 24 )EJ8 - 241 - 17
2626chain 'E' and (resid 25 through 50 )EJ25 - 5018 - 43
2727chain 'E' and (resid 51 through 108 )EJ51 - 10844 - 101
2828chain 'E' and (resid 109 through 130 )EJ109 - 130102 - 123
2929chain 'E' and (resid 131 through 147 )EJ131 - 147124 - 140
3030chain 'E' and (resid 148 through 162 )EJ148 - 162141 - 155
3131chain 'E' and (resid 163 through 174 )EJ163 - 174156 - 167
3232chain 'E' and (resid 175 through 216 )EJ175 - 216168 - 209
3333chain 'E' and (resid 217 through 235 )EJ217 - 235210 - 228

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