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- PDB-8bcq: N-terminal domain of Plasmodium berghei glutamyl-tRNA synthetase ... -

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Basic information

Entry
Database: PDB / ID: 8bcq
TitleN-terminal domain of Plasmodium berghei glutamyl-tRNA synthetase (native crystal structure)
ComponentsGlutamate--tRNA ligase
KeywordsRNA BINDING PROTEIN / aminoacyl-tRNA synthetase / tRNA / protein complex / Cell surface protein / multi-aminoacyl-tRNA synthetase complex (MARS-MSC) / GST-like domain / aminoacyl-tRNA synthetase-interacting multifunctional proteins (AIMP)
Function / homology
Function and homology information


glutamate-tRNA ligase / glutamate-tRNA ligase activity / glutamyl-tRNA aminoacylation / ATP binding / cytoplasm
Similarity search - Function
Glutamyl-tRNA synthetase, archaeal/eukaryotic cytosolic / Glutamyl/glutaminyl-tRNA synthetase, class Ib, anti-codon binding domain / tRNA synthetases class I (E and Q), anti-codon binding domain / Glutamyl/glutaminyl-tRNA synthetase / Glutamyl/glutaminyl-tRNA synthetase, class Ib, catalytic domain / tRNA synthetases class I (E and Q), catalytic domain / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / Glutathione S-transferase, C-terminal domain superfamily / Rossmann-like alpha/beta/alpha sandwich fold ...Glutamyl-tRNA synthetase, archaeal/eukaryotic cytosolic / Glutamyl/glutaminyl-tRNA synthetase, class Ib, anti-codon binding domain / tRNA synthetases class I (E and Q), anti-codon binding domain / Glutamyl/glutaminyl-tRNA synthetase / Glutamyl/glutaminyl-tRNA synthetase, class Ib, catalytic domain / tRNA synthetases class I (E and Q), catalytic domain / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / Glutathione S-transferase, C-terminal domain superfamily / Rossmann-like alpha/beta/alpha sandwich fold / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily
Similarity search - Domain/homology
glutamate--tRNA ligase
Similarity search - Component
Biological speciesPlasmodium berghei ANKA (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsBenas, P. / Jaramillo Ponce, J.R. / Frugier, M. / Sauter, C.
Funding support France, 3items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-10-IDEX-0002 France
Agence Nationale de la Recherche (ANR)ANR 20-SFRI-0012 France
Agence Nationale de la Recherche (ANR)ANR-17-EURE-0023 France
Citation
Journal: Protein Sci. / Year: 2023
Title: Solution X-ray scattering highlights discrepancies in Plasmodium multi-aminoacyl-tRNA synthetase complexes.
Authors: Jaramillo Ponce, J.R. / Theobald-Dietrich, A. / Benas, P. / Paulus, C. / Sauter, C. / Frugier, M.
#1: Journal: J.Biol.Chem. / Year: 2022
Title: Discovery of two distinct aminoacyl-tRNA synthetase complexes anchored to the Plasmodium surface tRNA import protein.
Authors: Jaramillo Ponce, J.R. / Kapps, D. / Paulus, C. / Chicher, J. / Frugier, M.
History
DepositionOct 17, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamate--tRNA ligase
B: Glutamate--tRNA ligase
C: Glutamate--tRNA ligase
D: Glutamate--tRNA ligase
E: Glutamate--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,75832
Polymers148,2395
Non-polymers2,51827
Water28816
1
A: Glutamate--tRNA ligase
hetero molecules

A: Glutamate--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,34624
Polymers59,2962
Non-polymers2,05022
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
MethodPISA
2
B: Glutamate--tRNA ligase
C: Glutamate--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,69717
Polymers59,2962
Non-polymers1,40115
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
D: Glutamate--tRNA ligase
E: Glutamate--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3883
Polymers59,2962
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7990 Å2
ΔGint-124 kcal/mol
Surface area19550 Å2
MethodPISA
4
A: Glutamate--tRNA ligase
B: Glutamate--tRNA ligase
C: Glutamate--tRNA ligase
D: Glutamate--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,11031
Polymers118,5914
Non-polymers2,51827
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6210 Å2
ΔGint-103 kcal/mol
Surface area19900 Å2
5
A: Glutamate--tRNA ligase
B: Glutamate--tRNA ligase
C: Glutamate--tRNA ligase
D: Glutamate--tRNA ligase
E: Glutamate--tRNA ligase
hetero molecules

A: Glutamate--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,43044
Polymers177,8876
Non-polymers3,54338
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area2800 Å2
ΔGint-20 kcal/mol
Surface area20480 Å2
Unit cell
Length a, b, c (Å)129.979, 88.683, 169.284
Angle α, β, γ (deg.)90.000, 106.130, 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
11A-401-

HOH

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Components

#1: Protein
Glutamate--tRNA ligase


Mass: 29647.863 Da / Num. of mol.: 5 / Mutation: A2, B2, C2, D2, E2: insertion (cloning artifact)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium berghei ANKA (eukaryote) / Strain: Anka / Gene: PBANKA_1362000 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A509AR09, glutamate-tRNA ligase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
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: 3.16 Å3/Da / Density % sol: 61.1 %
Description: Small and fragile crystals initially diffracting only at 5 angstroms were obtained. Their diffraction limit was further improved up to 2.7 angstroms by microseeding.
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein concentration: 6 to 9 mg/mL 0.1 M HEPS-NaOH pH 7.5, 1.4-1.5 M ammonium sulfate, 20% (v/v) glycerol and using microseeding.
Temp details: use of incubators

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 11, 2020 / Details: Kirkpatrick-Baez mirrors
RadiationMonochromator: channel cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.7→47.16 Å / Num. obs: 50722 / % possible obs: 99.69 % / Redundancy: 7 % / Biso Wilson estimate: 82.29 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.07188 / Rpim(I) all: 0.02919 / Rrim(I) all: 0.07767 / Net I/σ(I): 14.81
Reflection shellResolution: 2.703→2.799 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.181 / Mean I/σ(I) obs: 1.47 / Num. unique obs: 4911 / CC1/2: 0.759 / CC star: 0.929 / Rpim(I) all: 0.4809 / Rrim(I) all: 1.277 / % possible all: 97.73

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Processing

Software
NameVersionClassification
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
PHENIXdev_4701phasing
PHENIXdev_4701refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8BHD
Resolution: 2.7→47.16 Å / SU ML: 0.4038 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.4257
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2336 2535 5 %
Rwork0.1993 48153 -
obs0.201 50688 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 121.4 Å2
Refinement stepCycle: LAST / Resolution: 2.7→47.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8433 0 154 16 8603
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00158753
X-RAY DIFFRACTIONf_angle_d0.376111789
X-RAY DIFFRACTIONf_chiral_restr0.03891287
X-RAY DIFFRACTIONf_plane_restr0.00231443
X-RAY DIFFRACTIONf_dihedral_angle_d11.7263202
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.750.42481260.42792518X-RAY DIFFRACTION95.87
2.75-2.810.37031440.32972709X-RAY DIFFRACTION100
2.81-2.870.27261490.29342615X-RAY DIFFRACTION99.93
2.87-2.940.31281460.26812667X-RAY DIFFRACTION99.93
2.94-3.010.26131440.24632667X-RAY DIFFRACTION99.89
3.01-3.090.2621290.23812682X-RAY DIFFRACTION99.96
3.09-3.180.30951400.24732664X-RAY DIFFRACTION100
3.18-3.290.32341390.26782694X-RAY DIFFRACTION99.82
3.29-3.40.28871390.23122659X-RAY DIFFRACTION99.96
3.4-3.540.24091400.21992680X-RAY DIFFRACTION100
3.54-3.70.23021430.1972673X-RAY DIFFRACTION99.96
3.7-3.90.24441380.18462686X-RAY DIFFRACTION99.96
3.9-4.140.20681450.18862692X-RAY DIFFRACTION100
4.14-4.460.18671430.16712672X-RAY DIFFRACTION100
4.46-4.910.18791380.1642716X-RAY DIFFRACTION100
4.91-5.620.2251440.18412694X-RAY DIFFRACTION99.96
5.62-7.070.24961420.21532706X-RAY DIFFRACTION100
7.08-47.160.21041460.1712759X-RAY DIFFRACTION99.49
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)
11.845748037510.401834615205-0.3982230592580.9665063001210.07359324603473.55725248010.159525326831-0.181362955269-0.285955472785-0.0296112625606-0.1035955947760.03225398400750.2054737637860.245784913949-2.06370133532E-50.57860481603-0.0420505281362-0.05907495766020.4982480047440.1038923360240.77290910610243.069527583321.277191136294.2548005406
23.41100367779-0.646124347187-0.2438070023811.481415881410.01732989550420.6109697447430.137268736969-0.2238135377820.16883706868-0.00567599046405-0.07029861497390.00596215240506-0.136880947739-0.1884616159426.18814366074E-50.584231909795-0.08448562108180.06676529099310.5297928025340.007001233435550.63309998270627.063213105930.944978373492.9841777925
30.244892425256-0.6118466450660.2684262863252.23792931773-0.1770291038862.210121705190.14874343408-0.165436600416-0.14941880365-0.00880536267243-0.09927549658020.3337871725810.248919630565-0.0487178947443.03804508432E-60.566550436920.0585518603526-0.009433607595790.567275331381-0.007393466392770.74484801057411.531372934239.296162937369.7746879857
40.358914542060.103102308631-0.06711503211-0.002638443320150.0163705990305-0.01302430471510.5582179318230.02711304019790.746091363903-0.695655724733-0.4703849707490.287516533207-0.330578806787-0.385412153984-0.0006922844720710.7403396615570.258455861453-0.1498571134950.822391072645-0.01059971424651.13664673123-0.56632982235252.548282663857.2515668829
50.391012236035-0.4543343311750.07238094119390.2673380485720.406414397160.739219389154-0.01201928959770.6476826507610.317816856577-0.557753529360.0951002047807-0.556135080245-0.2247636099620.9004017356365.45158723726E-50.5785684385930.1072859468260.05377752503780.6727779116830.02993890645930.96937905805717.07558370660.972991083664.3002547402
60.713554796339-1.37910853248-0.8032904166242.562116202391.275050688010.895675424205-0.26711719139-0.2586531030450.4383497205270.3816472477690.0871636927616-0.188482610154-0.104810376125-0.003077165943132.19994142353E-50.5902095548250.08879694527890.00878380377280.617828355062-0.03204004220410.81553404720410.471240619859.2762588376.5956651965
70.09821035229250.239062923409-0.4390936449490.756859252242-0.643964210140.9240787555370.2567177942051.053167180240.836076194239-0.906757721216-0.04065409291140.104488903752-0.513631580722-0.1655909250410.002208882436521.063524483070.2603687437340.07718359591371.047278858950.2971143655361.0165838208415.48545576556.363352291840.83109475
81.13710094281-0.0315684257959-0.849135395510.209379618369-0.04938720121060.4946144896550.3644065961890.9146051049790.111983056787-0.0688168849278-0.3668476799080.6927731344350.19441797988-0.131019804421-2.70174195786E-50.7898689644790.242844070601-0.08161592542260.9447548678250.04828143610620.87892680730110.599216526346.237012201849.6327166714
91.54627130279-0.248707497644-0.9129469467491.009697190930.4704279602951.905045489150.4274314681120.1610199190160.0787450637992-0.228906765635-0.162133920561-0.1886832485270.2756321924070.3383929024560.03239565464430.76833407110.339593924340.06866903292570.9166752789460.01333286806750.60901009509928.409380001640.802075474244.9519691276
101.209558152980.694021216484-0.3143424111080.552424456278-0.4701357517440.007518514430760.185837513217-0.0671791342090.05777014413330.6042438282370.2977900262910.1812476249910.488693888112-0.1643021906635.52718095825E-51.61992484557-0.0437047959148-0.2449014685761.123570234850.0848089236561.00994212323.1783801956211.28723866532.0856332727
111.460333374521.16719172519-0.289020334231.17310187926-0.4189363144920.2351070881770.3749212907980.9812852564630.743693531051-0.2992662301070.4168298549990.2129376822971.133702999481.061199953210.07707625517411.477991435010.281491099894-0.1610406419691.42710702877-0.03220480631711.026363620816.516721554423.798793008225.1377495831
120.822479275690.134814327707-0.2448545898010.9021439003340.9848603583751.176804402480.4765541252520.324342663741-0.1759206850030.214881396424-0.246893551434-0.7296178451350.8847674515240.6286663501050.001255276597371.643122346070.362455008547-0.242592535861.08193622487-0.06538174419710.72126023280722.075153416914.771983498941.0431730135
13-0.0594742684146-0.00322300174136-0.004292018049730.0218889528669-0.0192932885414-0.06662206526740.7777304529240.8155189658070.131872006475-0.6118804313280.25099809986-0.892889805999-0.5449595503270.1308052778430.0001657065697841.638540998380.354110786745-0.09302127881652.11130369689-0.3774213259611.2126131962628.124270975418.10456786198.40216649683
142.448684841541.28360737527-0.7974354157120.649873065955-0.3860230468190.2185570528790.100954091170.7045298020770.9317776010260.03802561074230.742037741202-0.02825403438970.380317158870.7492111622060.1608285729162.114533325850.222828580119-0.3234086989371.94127669249-0.1179466292631.0404977524714.731576158222.63706427882.41283149159
150.1193701743220.2312444425180.2593975976740.2876626831850.2573211476250.0716086143837-0.04948710966970.842739182424-0.5403277899730.4351333381770.6830453111850.7749071657520.2660034433930.427814328508-0.0001461981122821.80902891530.27018208349-0.05908965698041.981549882360.04590368218961.3191755813224.35758155622.22886577886.74384910748
16-0.009708006978350.0243801832454-0.04454017574720.1065703495420.07859978433470.095480663780.952429219961-0.2038870678870.355305408084-0.904759890032-0.5469220530290.325923050730.1438997468010.2810151745014.69221249033E-51.681761059650.212650624086-0.1230670794211.680681000820.006428898209430.92763037634221.953623158820.405057123515.4654142563
170.01155466580140.0114111809241-0.0103377197658-0.07122834408570.04513284179270.030776235438-0.4318610864870.6436032045940.766992640544-0.458004574893-0.550267552897-0.0782795382842-0.246181313472-0.502578480787-0.0002085943507921.705343444080.292999287642-0.4596535844471.52078760835-0.05541320721911.089946135664.6664839793920.017807599812.9357729752
180.06675049954780.0446867083605-0.1324719673060.0267432819933-0.1026496464550.08645783203890.0002139948650020.0793876447181-0.8415556040080.6937787158920.2433757197780.6040332361110.399880463463-0.7637675829650.0001114956037382.193857878730.0919038377846-0.3891129249941.48839140741-0.03551982324341.282760691856.257841839249.3455559185517.4004561691
190.00731734858075-0.04673951870730.003810932744750.0688178669495-0.05261324387560.011564905395-1.164777344310.0790124496125-0.756646821789-0.190853495641.16026866110.469452355638-0.03866638588840.03144547800720.0001524997096652.396624588930.364180932983-0.2466941206741.9730796892-0.4611215987481.4147591698513.7787555863-4.384877755249.92639064313
200.0281214789210.05562979567610.0408580194370.04496837851420.03647251874320.01536869889420.126398232254-0.337766810432-0.0964952553082-0.1834481532760.002065676667740.1436735959520.790129024227-0.382790692736.79084719417E-52.507050939890.0338696459452-0.3877795860331.629321229390.02032560004510.8724489639021.375865101317.916171420217.19189687317
210.1341948324660.0298062603063-0.068384828650.0529852218243-0.05052996404820.0111833280722-0.6206983469740.918334165139-0.7597668420370.4134170204120.251373218105-0.17727656912-0.270459497941-0.220415991503-0.004509050152442.571863841060.291527362342-0.3381444411271.77130165851-0.3268299845091.1245214608816.24053541353.87897692392.44136383528
22-0.01086486938240.000335971849494-0.00035520386929-0.0112275021980.00283455164395-0.002419858470540.322748799671-0.4555080171130.273008593586-0.106264031941-0.472966797996-0.280442116032-0.06521966943420.0717997438486-5.62011822769E-53.38633398465-0.0599089216043-0.6398432309361.9741362229-0.3765296003411.5290209419615.6352309443-7.6289996925-3.15598251817
231.098298037740.484277183682-0.3366239107930.258900978074-0.1289589063860.0709589874543-0.8427070450870.101653983899-0.5394737471470.1941489127050.239364792591-0.276227613601-0.1068802664470.392194654669-0.05850129732592.546916139820.447660549298-0.3597983048912.10411023365-0.4775148926011.02976931637.652488026763.27228045965-1.91699922128
241.865734202972.424156266920.2147910400143.207195791620.2889234943760.0151053688512-0.4936338234180.5478963900821.05414589474-0.2105177494750.2183644883981.20980797997-0.076358478114-0.551522395919-0.008072575101441.97484143382-0.2019665169910.1401518742762.53688029016-0.1119619075960.22889394105820.852923927414.0693407289-4.14465150555
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 116 )AA5 - 1161 - 86
22chain 'A' and (resid 117 through 227 )AA117 - 22787 - 197
33chain 'B' and (resid 5 through 99 )BB5 - 991 - 75
44chain 'B' and (resid 100 through 116 )BB100 - 11676 - 92
55chain 'B' and (resid 117 through 153 )BB117 - 15393 - 129
66chain 'B' and (resid 154 through 227 )BB154 - 227130 - 203
77chain 'C' and (resid 6 through 66 )CC6 - 661 - 52
88chain 'C' and (resid 67 through 116 )CC67 - 11653 - 87
99chain 'C' and (resid 117 through 227 )CC117 - 22788 - 198
1010chain 'D' and (resid 7 through 99 )DD7 - 991 - 72
1111chain 'D' and (resid 100 through 134 )DD100 - 13473 - 104
1212chain 'D' and (resid 135 through 226 )DD135 - 226105 - 196
1313chain 'E' and (resid 7 through 17 )EE7 - 171 - 11
1414chain 'E' and (resid 18 through 34 )EE18 - 3412 - 28
1515chain 'E' and (resid 35 through 60 )EE35 - 6029 - 47
1616chain 'E' and (resid 61 through 99 )EE61 - 9948 - 72
1717chain 'E' and (resid 100 through 115 )EE100 - 11573 - 82
1818chain 'E' and (resid 116 through 133 )EE116 - 13383 - 100
1919chain 'E' and (resid 134 through 155 )EE134 - 155101 - 122
2020chain 'E' and (resid 156 through 166 )EE156 - 166123 - 133
2121chain 'E' and (resid 167 through 184 )EE167 - 184134 - 151
2222chain 'E' and (resid 185 through 194 )EE185 - 194152 - 161
2323chain 'E' and (resid 195 through 207 )EE195 - 207162 - 174
2424chain 'E' and (resid 208 through 224 )EE208 - 224175 - 191

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