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- PDB-8us8: Crystal structure of B1E11K malarial antibody in complex with RES... -

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Basic information

Entry
Database: PDB / ID: 8us8
TitleCrystal structure of B1E11K malarial antibody in complex with RESA repeat peptide
Components
  • (B1E11K Fab A ...) x 2
  • Ring-infected erythrocyte surface antigen peptide
KeywordsIMMUNE SYSTEM / malaria / antibody / homotypic
Function / homology
Function and homology information


DNAJ-containing protein, X-domain / : / X-domain of DnaJ-containing / Plasmodium RESA, N-terminal / Plasmodium RESA, N-terminal helical domain superfamily / Plasmodium RESA N-terminal / Nt-dnaJ domain signature. / DnaJ domain, conserved site / DnaJ domain / DnaJ molecular chaperone homology domain ...DNAJ-containing protein, X-domain / : / X-domain of DnaJ-containing / Plasmodium RESA, N-terminal / Plasmodium RESA, N-terminal helical domain superfamily / Plasmodium RESA N-terminal / Nt-dnaJ domain signature. / DnaJ domain, conserved site / DnaJ domain / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain
Similarity search - Domain/homology
Ring-infected erythrocyte surface antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
Plasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 Å
AuthorsYoo, R. / Julien, J.P.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Elife / Year: 2025
Title: Target-agnostic identification of human antibodies to Plasmodium falciparum sexual forms reveals cross-stage recognition of glutamate-rich repeats.
Authors: Amen, A. / Yoo, R. / Fabra-Garcia, A. / Bolscher, J. / Stone, W.J.R. / Bally, I. / Dergan-Dylon, S. / Kucharska, I. / de Jong, R.M. / de Bruijni, M. / Bousema, T. / King, C.R. / MacGill, R.S. ...Authors: Amen, A. / Yoo, R. / Fabra-Garcia, A. / Bolscher, J. / Stone, W.J.R. / Bally, I. / Dergan-Dylon, S. / Kucharska, I. / de Jong, R.M. / de Bruijni, M. / Bousema, T. / King, C.R. / MacGill, R.S. / Sauerwein, R.W. / Julien, J.P. / Poignard, P. / Jore, M.M.
History
DepositionOct 27, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: B1E11K Fab A Heavy Chain
L: B1E11K Fab A Kappa Light Chain
A: B1E11K Fab A Heavy Chain
B: B1E11K Fab A Kappa Light Chain
R: Ring-infected erythrocyte surface antigen peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,59310
Polymers96,1465
Non-polymers4465
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11210 Å2
ΔGint-89 kcal/mol
Surface area38030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.704, 186.289, 131.517
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

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Protein/peptide , 1 types, 1 molecules R

#3: Protein/peptide Ring-infected erythrocyte surface antigen peptide


Mass: 2131.121 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Plasmodium falciparum (malaria parasite P. falciparum)
References: UniProt: P13830

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Antibody , 2 types, 4 molecules HALB

#1: Antibody B1E11K Fab A Heavy Chain


Mass: 23365.176 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody B1E11K Fab A Kappa Light Chain


Mass: 23642.375 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Non-polymers , 3 types, 135 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 2.56 Å3/Da / Density % sol: 51.92 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium acetate pH 5.2, 0.1 M NH4)2SO4, 25% (w/v) PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.56→39.67 Å / Num. obs: 31520 / % possible obs: 99.8 % / Redundancy: 7.5 % / Biso Wilson estimate: 65.06 Å2 / CC1/2: 0.99 / Net I/σ(I): 10.8
Reflection shellResolution: 2.56→2.65 Å / Num. unique obs: 3067 / CC1/2: 0.365

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.56→39.67 Å / SU ML: 0.3766 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.5666
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2477 1575 5 %
Rwork0.2157 29939 -
obs0.2173 31514 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 89.75 Å2
Refinement stepCycle: LAST / Resolution: 2.56→39.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6627 0 24 130 6781
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00176796
X-RAY DIFFRACTIONf_angle_d0.46879233
X-RAY DIFFRACTIONf_chiral_restr0.04121031
X-RAY DIFFRACTIONf_plane_restr0.00451187
X-RAY DIFFRACTIONf_dihedral_angle_d10.15212437
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.56-2.640.35511390.35112639X-RAY DIFFRACTION98.27
2.64-2.740.34551420.32862714X-RAY DIFFRACTION99.96
2.74-2.850.30831400.31132654X-RAY DIFFRACTION99.96
2.85-2.980.38221430.30632713X-RAY DIFFRACTION99.96
2.98-3.130.341430.28392709X-RAY DIFFRACTION99.96
3.13-3.330.3051410.26512692X-RAY DIFFRACTION99.89
3.33-3.590.26791430.2392722X-RAY DIFFRACTION100
3.59-3.950.22511440.20322723X-RAY DIFFRACTION99.97
3.95-4.520.21331430.17262725X-RAY DIFFRACTION99.93
4.52-5.690.19121450.16862778X-RAY DIFFRACTION99.9
5.69-39.670.2211520.192870X-RAY DIFFRACTION99.74
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)
10.0576080192793-0.0220716702080.00070730838093-0.00615858188571-0.02965231757520.0312569769356-0.005153013105750.0127902214778-0.0994528322350.12076178894-0.0651226202113-0.0164207717545-0.0227594439959-0.01985271915614.93655292840.6216216397440.0230737129153-0.0247333920440.2788989492870.09767626010460.26746529371321.006-16.63924.051
20.009876625765220.0358568662032-0.05886782406990.01776047246440.00361472775615-0.01734488631890.1903636618840.05182203860110.01712451066280.08655957381050.321027197595-0.02924682074550.0127275885154-0.111924336238-3.080206767590.346301139870.1635327284560.004315247315770.377437746754-0.002734105141020.18532827200515.695-6.39430.326
30.07132841381420.02078229308620.08813892181110.148707571618-0.06786384363840.01803832251480.0514505090630.1443336929290.03879375144120.113954630193-0.0186528120577-0.15124268240.0199439378753-0.09653770153047.448483089330.4154913140840.05581774199350.008355792825610.3770568865470.01277895693940.26965235345715.625-7.05919.651
40.01138339548150.084604700073-0.0521946786974-0.0459194889385-0.003197638743060.048665973735-0.08189213826490.00411533732661-0.0594673385580.07212065055480.322423203926-0.005596046058780.00820263247275-0.0675258633123-1.4170763010.4724836835010.0396379975385-0.07873605558980.408173353781-0.04960851431010.28070959968922.523-9.18120.208
5-0.00973669581456-0.0175517582615-0.0185097268248-0.09485612337920.024241535235-0.02632391612170.0956133681378-0.120363425769-0.281261789884-0.116367930448-0.244956708755-0.4093492449740.149067058045-0.602845402058-1.034938128660.5130068557860.08630951447920.04695025826450.05443471278730.03793837366380.61920140187141.236-28.60811.1
60.02249577982340.0683852627119-0.02670705400150.1487006598620.08834979499420.06013703988610.0769501113892-0.02659792805110.0842829669262-0.0883966098219-0.310074494988-0.454153099348-0.0489144702597-0.3990248695774.604365951640.5754205183070.0798789503802-0.009051039133750.4403657847450.07748749123170.87330727771647.266-26.26514.506
70.00964332323825-0.00125288163365-0.02561446745540.0273951460817-0.0037157971791-0.037506404433-0.0619338042807-0.008195959970230.02525657445-0.054027815523-0.179488787638-0.3148601224460.139888411745-0.2815111301454.646801816630.6122952842860.1711680826190.06674488216380.4036729418310.04596766948620.98316484457646.404-34.47917.315
80.0897305136462-0.159550294947-0.1359023543340.2661985192480.03392424759940.253947524812-0.03061449724110.006666428320080.0289665016885-0.02817582992210.0124281881472-0.23785445192-0.0102059226632-0.1379623729731.878191330160.3563470818810.0605843010146-0.05633267685020.396749617945-0.06467410820310.49825486959133.6796.32717
9-0.006241311252330.0226719532409-0.03082352101010.02045474447120.0143627327648-0.0170889855599-0.275265659381-0.09153588142320.108453479387-0.203152517691-0.117626592281-0.06022082355820.0995047587497-0.07053188218791.19270878128-0.3454821481150.3099386303450.4243673516840.201857530296-0.05218350034541.1061329176653.284-5.3069.784
100.0132319402185-0.0147331759727-0.02463631947770.00623706751970.0223551298948-0.03619911637240.148909396117-0.1364348736010.1908348210950.02596956646840.139614976837-0.165285927540.325146226247-0.299573699538-1.134511319891.001215902140.2488350646350.4074594135810.505744463737-0.2031343434811.25538669148.945-34.2172.053
11-0.005535006691180.0626742325370.004888671339760.00859538593465-0.01841879939760.0457575970923-0.299345327035-0.03021165463310.355734217005-0.09194588524-0.5074514568650.04209884028360.3751327152320.1884643313662.351417947870.3334072850340.1684802545990.2878428461390.4658611154060.09791345187151.2355571722450.239-16.2924.591
12-0.00338674828502-0.002337595538460.004267390959940.00244509393298-0.002754198949470.000571399389408-0.1425773492820.0576032010122-0.02859332321840.03013107179490.004180469960590.09029095172220.005547822864210.034044918285.052330362981.25552284190.2003008472230.5664815218151.02043469035-0.09415006569270.66469940624847.656-20.367-9.643
130.122212983188-0.08374336085530.02592923395220.05940708611050.03178881364550.0237466726994-0.133861893006-0.220020881415-0.14334817189-0.312224059615-0.195634289786-0.477107843338-0.0163821769435-0.326467071546-1.81760944180.6012896985630.1210770388150.3316902152190.499582832922-0.02454857344930.97660649349949.952-20.571-0.514
140.0159277582152-0.049408666837-0.05383102870350.002349984909840.04391878305380.03976156503190.1527610284610.04198557125370.02629847912720.007513187735360.265990403179-0.0288523673903-0.0293340726683-0.1353380168551.099241868160.4124286120540.06133542580920.03659458936450.3626680673830.02926481224560.390911961414.337.3618.096
150.02880252375830.02516165473260.006639530737630.0258779848138-0.005257769897550.0030972535753-0.0818068378041-0.117126609432-0.256146049388-0.1314943492150.226127596886-0.0262183498375-0.2652206539870.173253479876-7.081256368170.3912073297550.0223568857341-0.0171232412190.3069085126650.0134865939260.27839119954413.82128.5546.994
160.01351689531720.0421158220952-0.008604106327440.03176658321130.0222202644450.00658998507387-0.1601654779940.156272245176-0.07702892384680.1679525006060.3335742329210.0731385473897-0.129394850803-0.04220568316554.519379380570.3334755107190.08316636381340.05124246250720.418848750695-0.004172634211030.408936121352-1.6626.6636.788
170.08790405210480.0350272103306-0.03676225001610.2280398099950.01841439128990.06532691068710.05190370727150.0741633763380.006976163315510.02657769781160.03140204342420.0260788763743-0.0513274594923-0.0232916646985-4.644445595830.3989944401620.03430354419350.02195494270260.393429462070.04063206698380.3266244240525.37728.522.448
180.0643916022565-0.0586498898161-0.07680322742060.2329200635450.09730094908110.05042742699970.0659657315407-0.0858337071179-0.150943737608-0.00476254888442-0.2702174101750.283543742716-0.1396938488690.3460729715951.215298596470.4942940796680.04699630433270.08485026487560.4707152375110.03752561526750.482387125743-12.09244.27125.753
19-0.03665038182260.0187735985679-0.00669276610148-0.009249587467260.02084030115070.00945679824813-0.1606041478920.02307053204220.09390324482350.081038920782-0.278338890248-0.164944815383-0.0116238455764-0.0814727780207-3.770941496730.6501403885070.006529097904190.1047120778840.480577670751-0.1475270342020.421722630196-7.75850.71828.483
200.0192955624561-0.00439437982288-0.00377344984840.03954328676570.05358958952410.02865109467170.1427567774270.02349936899510.001037851512040.07278189959660.2961525973370.2987883781750.07097711559460.121713121047-1.56229679040.3242432311060.07314836543830.1820524450680.3897794318540.1798192149430.280766662326-12.45412.14116.511
210.09645156551860.0300782689001-0.03047155877760.0301446343821-0.006283477197990.01448025920710.10447595332-0.0633628267534-0.0925080033494-0.06222065038730.1553091700730.0358421401102-0.0594039026461-0.0182145717133-8.95665773780.3080282054730.05645931881140.03506377675030.3158663632180.04516705242230.299798347213-2.23210.53115.397
220.04243182910620.03712598322570.01888184074070.03905092942040.0177901905480.00506357533768-0.3087829785010.0757847810285-0.02068701340250.0937935893370.2941999702280.56468267835-0.1340178671270.2778546726755.415591552040.4551077078210.07123289453990.2208374646870.355153225790.04731562805790.339633486035-6.06415.09822.538
230.00684203841660.01621183068960.00741909717166-0.01056602597110.03289496879890.00271466355050.0340263432879-0.08176778669560.201138427701-0.0852376579583-0.129435514586-0.04741501640060.1091194417150.008391444099757.345902353750.2990356464780.0681525095126-0.007436361441480.4539698272460.02533436907470.467264684468-2.55115.9495.316
240.007254174598930.01646768953290.004277869826280.0007134430598250.009531355788340.004429586714410.3150441283130.0736841245405-0.04116904196690.1731902641490.134783932760.1412320829130.1475785321350.152349287765-1.640643738540.4593692973-0.1162186668280.8247927989860.5225470720050.4381931880570.554158561638-18.54120.9130.923
250.00416455588858-0.0142469803123-0.0465960277138-0.00229095901933-0.020128280329-0.0302125271656-0.249584271965-0.1691525243840.2640373563980.026988350077-0.2279081868880.0380836929998-0.0283926415804-0.09272736053881.069916335930.8229939986590.05967886016110.3356544769810.6512563407860.03463605154661.39998194697-23.15850.72728.876
260.0137738987280.00646076288662-0.0330123206790.0246341396019-0.00743230317072-0.02091556277990.0466409681342-0.0673882685947-0.035738432133-0.015881371466-0.1459448912760.162967878773-0.04373448003510.0346711727011-4.162426588510.670538698040.03974457666190.3933727601590.673264765448-0.02620005991581.2272629963-26.12635.66827.652
270.02811038979580.0345298008457-0.03878677956730.0438717476501-0.05661478219450.0347603391294-0.141662414753-0.09144738057730.146570018709-0.00585596239625-0.1896330478260.2102525988120.03997533208630.2307557347317.977622142440.64455603960.01311040275480.1471389222610.878432092193-0.07589520209610.961569735787-23.24134.39625.742
280.0216662057050.02543907435860.02584101059150.01089635272270.03639546873160.0586027894558-0.1905013238430.01637069717390.173237489132-0.0494444613772-0.1790734630760.1335001461360.0735760307387-0.065390427894-1.477103988920.4722771808430.366866802140.7099880415070.619296165498-0.1354779652491.29771511837-30.15245.47325.161
290.01795732574770.022507400373-0.05492926161940.00449723256096-0.000860960517024-0.00558874263596-0.0518680325338-0.006829991523110.197486280681-0.126438241110.04816347726780.0714572220645-0.02201554519220.07150105590763.196276679680.9678729129090.07482194814831.832059839760.866906953159-0.3300047534981.63182656425-32.20139.36333.841
300.0320714652779-0.0156805926109-0.0113960820140.01408184529880.01127285074430.0103986237606-0.0083293900444-0.01773993953780.101599449790.0241605731213-0.1813744575630.07300295738140.05509413019570.00709912316013-2.838564262790.6154111516740.0311001205647-0.01056543885620.4795914360250.007073939770190.44429234653314.6319.51419.745
310.005564890054970.00652610282798-0.000466611971572-0.001168458479880.01427434391820.00700325699154-0.1102680278570.0157591523120.0297819153255-0.174061051545-0.0479969098075-0.01073469964890.04565879618310.00653755446155-2.076752022290.405140791976-0.107369748995-0.001773129730260.3752283190590.01972587139760.2887609841428.40511.973-0.651
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN H AND RESID 1:17 )H1 - 17
2X-RAY DIFFRACTION2( CHAIN H AND RESID 18:33 )H18 - 33
3X-RAY DIFFRACTION3( CHAIN H AND RESID 34:82 )H34 - 82
4X-RAY DIFFRACTION4( CHAIN H AND RESID 83:106 )H83 - 106
5X-RAY DIFFRACTION5( CHAIN H AND RESID 107:143 )H107 - 143
6X-RAY DIFFRACTION6( CHAIN H AND RESID 144:193 )H144 - 193
7X-RAY DIFFRACTION7( CHAIN H AND RESID 194:214 )H194 - 214
8X-RAY DIFFRACTION8( CHAIN L AND RESID 1:102 )L1 - 102
9X-RAY DIFFRACTION9( CHAIN L AND RESID 103:115 )L103 - 115
10X-RAY DIFFRACTION10( CHAIN L AND RESID 116:128 )L116 - 128
11X-RAY DIFFRACTION11( CHAIN L AND RESID 129:144 )L129 - 144
12X-RAY DIFFRACTION12( CHAIN L AND RESID 145:155 )L145 - 155
13X-RAY DIFFRACTION13( CHAIN L AND RESID 156:212 )L156 - 212
14X-RAY DIFFRACTION14( CHAIN A AND RESID 1:17 )A1 - 17
15X-RAY DIFFRACTION15( CHAIN A AND RESID 18:33 )A18 - 33
16X-RAY DIFFRACTION16( CHAIN A AND RESID 34:51 )A34 - 51
17X-RAY DIFFRACTION17( CHAIN A AND RESID 52:106 )A52 - 106
18X-RAY DIFFRACTION18( CHAIN A AND RESID 107:193 )A107 - 193
19X-RAY DIFFRACTION19( CHAIN A AND RESID 194:214 )A194 - 214
20X-RAY DIFFRACTION20( CHAIN B AND RESID 1:18 )B1 - 18
21X-RAY DIFFRACTION21( CHAIN B AND RESID 19:75 )B19 - 75
22X-RAY DIFFRACTION22( CHAIN B AND RESID 76:90 )B76 - 90
23X-RAY DIFFRACTION23( CHAIN B AND RESID 91:102 )B91 - 102
24X-RAY DIFFRACTION24( CHAIN B AND RESID 103:113 )B103 - 113
25X-RAY DIFFRACTION25( CHAIN B AND RESID 114:128 )B114 - 128
26X-RAY DIFFRACTION26( CHAIN B AND RESID 129:150 )B129 - 150
27X-RAY DIFFRACTION27( CHAIN B AND RESID 151:172 )B151 - 172
28X-RAY DIFFRACTION28( CHAIN B AND RESID 173:197 )B173 - 197
29X-RAY DIFFRACTION29( CHAIN B AND RESID 198:213 )B198 - 213
30X-RAY DIFFRACTION30( CHAIN R AND RESID 1:10 )R1 - 10
31X-RAY DIFFRACTION31( CHAIN R AND RESID 11:17 )R11 - 17

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