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- PDB-6ruu: Pseudokinase domain of human IRAK3 -

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Basic information

Entry
Database: PDB / ID: 6ruu
TitlePseudokinase domain of human IRAK3
ComponentsInterleukin-1 receptor-associated kinase 3Interleukin-1 receptor associated kinase
KeywordsSIGNALING PROTEIN / Pseudokinase / Homo-dimer / Innate Immunity
Function / homology
Function and homology information


positive regulation of macrophage tolerance induction / regulation of protein-containing complex disassembly / negative regulation of cytokine-mediated signaling pathway / negative regulation of macrophage cytokine production / negative regulation of protein-containing complex disassembly / response to peptidoglycan / Toll signaling pathway / negative regulation of toll-like receptor signaling pathway / negative regulation of interleukin-12 production / MyD88-dependent toll-like receptor signaling pathway ...positive regulation of macrophage tolerance induction / regulation of protein-containing complex disassembly / negative regulation of cytokine-mediated signaling pathway / negative regulation of macrophage cytokine production / negative regulation of protein-containing complex disassembly / response to peptidoglycan / Toll signaling pathway / negative regulation of toll-like receptor signaling pathway / negative regulation of interleukin-12 production / MyD88-dependent toll-like receptor signaling pathway / interleukin-1-mediated signaling pathway / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / response to exogenous dsRNA / negative regulation of NF-kappaB transcription factor activity / negative regulation of interleukin-6 production / negative regulation of tumor necrosis factor production / negative regulation of innate immune response / response to interleukin-1 / negative regulation of MAP kinase activity / positive regulation of cytokine production / response to virus / negative regulation of protein catabolic process / Interleukin-1 signaling / cytokine-mediated signaling pathway / positive regulation of NF-kappaB transcription factor activity / cellular response to lipopolysaccharide / response to lipopolysaccharide / intracellular signal transduction / protein heterodimerization activity / protein phosphorylation / protein serine/threonine kinase activity / protein kinase binding / magnesium ion binding / protein homodimerization activity / ATP binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Interleukin-1 receptor-associated kinase 3, pseudokinase domain / IRAK3, death domain / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Death-like domain superfamily / Protein kinase domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
: / Interleukin-1 receptor-associated kinase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsLange, S.M. / Kulathu, Y. / Cohen, P.
CitationJournal: Structure / Year: 2021
Title: Dimeric Structure of the Pseudokinase IRAK3 Suggests an Allosteric Mechanism for Negative Regulation.
Authors: Lange, S.M. / Nelen, M.I. / Cohen, P. / Kulathu, Y.
History
DepositionMay 29, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Dec 9, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Mar 17, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.year
Revision 1.4Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interleukin-1 receptor-associated kinase 3
B: Interleukin-1 receptor-associated kinase 3
C: Interleukin-1 receptor-associated kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,17822
Polymers108,5293
Non-polymers2,65019
Water0
1
A: Interleukin-1 receptor-associated kinase 3
B: Interleukin-1 receptor-associated kinase 3
hetero molecules


  • defined by author&software
  • Evidence: gel filtration, Wildtype protein elutes as concentration dependent equilibrium of dimer and monomer peaks (under reducing buffer conditions). Point mutation L210E shifts peak to monomer ...Evidence: gel filtration, Wildtype protein elutes as concentration dependent equilibrium of dimer and monomer peaks (under reducing buffer conditions). Point mutation L210E shifts peak to monomer only. Point mutation E214L shifts peak to dimer only.
  • 73.7 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)73,71513
Polymers72,3522
Non-polymers1,36211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint-186 kcal/mol
Surface area26000 Å2
MethodPISA
2
C: Interleukin-1 receptor-associated kinase 3
hetero molecules

C: Interleukin-1 receptor-associated kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,92718
Polymers72,3522
Non-polymers2,57416
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_465-x-1,-y+1,z1
Buried area4790 Å2
ΔGint-290 kcal/mol
Surface area23950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.550, 167.160, 179.510
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

#1: Protein Interleukin-1 receptor-associated kinase 3 / Interleukin-1 receptor associated kinase / IRAK-3 / IL-1 receptor-associated kinase M / IRAK-M


Mass: 36176.195 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IRAK3 / Plasmid: pFastBac
Details (production host): DU56013 (MRC PPU Reagents & Services)
Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9Y616, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Hg
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4

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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: 4.22 Å3/Da / Density % sol: 70.87 % / Description: Rod shaped
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 20C, 8mg/mL protein, hanging drop vapour diffusion, 2uL :1uL drop ratio (protein:precipitant) + 1mL reservoir, streak seeding from 1:100 seed stock (original seed stock: 10 uL from drops ...Details: 20C, 8mg/mL protein, hanging drop vapour diffusion, 2uL :1uL drop ratio (protein:precipitant) + 1mL reservoir, streak seeding from 1:100 seed stock (original seed stock: 10 uL from drops containing previously obtained crystals +50 uL precipitant mix, crushed by vortexing with seed bead, diluted in precipitant mix), crystals appeared after 2-3 days, harvested after 5-7 days, overnight soaking with 1:1 v/v of 5 mM Ethylmercury Phosphate in stabilising solution, Cryo: Precipitant mix +30% Glycerol

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: LN cryo stream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 1.007 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.007 Å / Relative weight: 1
ReflectionResolution: 2.5→49.056 Å / Num. obs: 28005 / % possible obs: 92.2 % / Observed criterion σ(I): 2 / Redundancy: 29.4 % / Biso Wilson estimate: 77.94 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.28 / Rpim(I) all: 0.052 / Rrim(I) all: 0.285 / Net I/σ(I): 12.1
Reflection shellResolution: 2.959→3.307 Å / Redundancy: 30.9 % / Rmerge(I) obs: 2.4 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1072 / CC1/2: 0.702 / Rpim(I) all: 0.438 / Rrim(I) all: 2.45 / % possible all: 59.6

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Processing

Software
NameVersionClassification
PHENIXrefinement
MxCuBEdata collection
XDS20190315data reduction
Aimless0.7.4data scaling
STARANISO1.0.4data scaling
MoRDaccp4-onlinephasing
BALBES1.1.5_DB_Nov_16_2011phasing
PARROT1.0.4phasing
Coot0.8.9.1 (revision-count 7414)model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QKW

2qkw


Resolution: 2.95→48.65 Å / SU ML: 0.2928 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.3969
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.26 1119 5.21 %
Rwork0.2283 20377 -
obs0.2299 21496 61.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 90.74 Å2
Refinement stepCycle: LAST / Resolution: 2.95→48.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6186 0 66 0 6252
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00336368
X-RAY DIFFRACTIONf_angle_d0.6278654
X-RAY DIFFRACTIONf_chiral_restr0.04361005
X-RAY DIFFRACTIONf_plane_restr0.00351084
X-RAY DIFFRACTIONf_dihedral_angle_d6.96873770
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-3.090.382390.4061211X-RAY DIFFRACTION5.15
3.09-3.250.3765260.333531X-RAY DIFFRACTION13.07
3.25-3.450.3505640.29571264X-RAY DIFFRACTION30.98
3.45-3.720.29871350.26622240X-RAY DIFFRACTION55.16
3.72-4.090.26171990.23593451X-RAY DIFFRACTION84.2
4.09-4.690.24182130.20274117X-RAY DIFFRACTION99.79
4.69-5.90.22942420.22054174X-RAY DIFFRACTION99.98
5.9-48.660.26922310.22654389X-RAY DIFFRACTION99.81
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)
14.45375776543-0.1550899737982.885665683251.021257074680.1028188108011.94475044012-0.2367416109630.3446514744950.232891625502-0.4256136971280.2446509974570.303188652824-0.30629166681-0.01236875725330.1489342830050.656915974546-0.191957655301-0.1768515728382.07082494607-0.0316792972120.601764600984-30.046684531337.7764694085-52.2484217208
22.68269739462-0.585686226899-1.298123047340.247168306119-0.2664974559733.61600555704-0.002979109152571.85726972245-0.313213623992-0.2571981318740.1294414908430.2775100241920.666339804522-0.680722425846-0.1266563807130.722771642906-0.3133599461690.01288984900640.928798206808-0.1487117180540.501133874025-26.37548368630.0061812202-38.8745097235
36.747320318940.609358948486-1.26419332313.11758938395-1.206689714242.986201655430.00498786215040.7591130023690.897102880866-0.33333047124-0.206834513461-0.289605041596-0.6729889752070.3606408313840.06256864454130.781914218514-0.110764275516-0.07451472417280.2375164344740.1512264017860.440634113128-15.80333495240.3658376047-29.8184273728
42.212338712842.402495131820.6162531829864.20628160969-0.0363215731083.41757940387-0.08308527646550.1243320948330.947542983067-0.3767919111-0.06856553139390.441177971359-0.505927510269-0.201612347294-0.02288005823680.7351173588980.09858016234720.119576333072-0.00322628712978-0.01377927570480.458809570159-26.235648944745.5767057816-18.9868950033
52.71686517503-0.15592417024-0.5740864251621.6873792184-0.7753488980880.667344587575-0.05867496331460.161404620085-0.8242483302810.284775899105-0.1173958127370.08993791698920.560050602214-0.2778613158490.09665747527380.856095613272-0.1530833557350.05144065427330.166377327157-0.002702437539120.504784499649-22.755996282329.7123371533-17.682554599
61.54890021381.921270429223.45293144322.403904899564.311871852167.748871418040.005612526480751.57417833726-1.26771432047-0.3200965456920.199344378543-0.7669574847961.665399074091.09358698477-0.1024046931441.711073301050.1832466685350.2176433554361.92805887278-0.4319401636111.32183596551-4.7804021057811.949015278-60.3695663107
73.028083789762.548228645684.447543409937.936094158724.214910999417.09332600265-0.5577927038641.62910598629-1.27894764348-0.7769465972310.31572239879-0.6759242754080.8143996567031.477724864850.1899953504221.29476676738-0.05481473657420.03508160515651.83590838525-0.2842296760121.00863550714-3.2910705571120.0755652071-59.6734321299
87.799302344291.12715006617-6.605693791783.44748417179-1.222911153245.616163413840.0921031887485-1.68764598618-0.1021966792240.391952112202-0.280660316923-0.542947982178-0.1185712238741.686216044270.1391110187360.678796262689-0.07937871423620.1897289795072.13485071861-0.04758858342870.608220216003-8.0316444853231.640346247-54.3859025738
91.44000305070.57766840658-0.7504494985627.025323406751.278672051395.644912582540.1161831836431.72977158446-0.443744309290.457219857574-0.447324271296-0.1802688429641.074916568780.1424059239980.2935119497340.802212319527-0.1392849714030.04525386764332.21683370172-0.1557039286660.825043619089-11.211953631424.535630695-64.6207998418
100.2515868247590.07554986884850.419456525670.1987928370250.004416722549840.785829936246-0.03020580007770.56591120573-0.248170724175-0.1744633563880.323429542933-0.05856385684440.1397163163980.4315105363580.001675422793110.475800970769-0.005322143972490.0396069545612.8397520282-0.03485649133020.638011076189-3.726006721834.9494857522-75.1869772994
115.18665792976-0.0211375369013-1.723628202691.972553197630.440958490693.447207504750.09521266931170.758767552216-0.36328263062-0.09792911370910.120508326604-0.0640466779116-0.01500782668650.485715848332-0.07232271900330.576806888446-0.2485987107680.03732028413962.41768628114-0.1385190313490.574218092788-6.8153633295333.926412559-67.8053253479
121.45766926525-1.279527791350.8449019418081.11748428771-0.7306836428671.55030927722-0.0776183877217-0.5459879119860.2520214638290.404638205927-0.0872397883651-0.310918342354-0.0920178665927-0.3136182759920.08554248897580.550140245476-0.156547914586-0.1561589622462.47973665150.3581802713140.7837607402463.8165621038342.9484812718-66.2158215886
138.189986493061.565420536110.4440098601872.63632085005-0.3672069181770.502439558381-0.1266396971480.326348926599-0.224333378562-0.1007350605590.152217502705-0.544057610411-0.0320970030709-0.0769650837475-0.07059487544560.5327917959490.1261508010130.06894476995162.615590911820.1024110951851.1491606858914.781879636441.8416355971-76.0834741074
140.974741511911-0.874219758526-1.957806989720.8056129827561.69808436654.517580636350.4271353384980.1240656561720.126804846848-0.173426978395-0.269505662646-0.232239767756-0.7119481085890.387641300623-0.23725223260.887707880068-0.205901232990.095654637073.147137306290.3099674156280.7968605939095.2862292143446.0284091295-83.3289581198
159.294431287150.9408739066248.193306998512.419731027040.0555088628027.479408210470.214029840644-0.816534110948-0.2492856724160.0996562744659-0.03823478616390.2652442399730.0378662415732-0.769739714553-0.0628880522080.650937746361-0.157234768471-0.1411273315812.545763675140.4075082820870.749576415811-7.4588667955744.6886746247-85.0966367305
163.076655166150.4191175105652.128859750634.298556634810.9791708511373.50879559888-0.4523962853530.3164747570030.5071016808990.190216201437-0.0736250036502-1.09494819559-0.7190482906290.7853170758090.4305753210571.22648317594-0.154282706786-0.09330478981670.66089338088-0.05318780719881.74838420606-18.054936739377.95270278588.18000227212
174.489282350453.83088706482-0.5667336911623.52106370574-0.3039128665320.562618401430.186548131392-0.3465744778390.5112176460840.454223617462-0.121914828219-0.254374614447-0.5354115376450.208735552138-0.124444531321.48133295659-0.0685336385871-0.02195803622280.256636417934-0.1178601334741.40151468681-23.134256496278.91341066812.8347072004
181.18929454266-0.877547616908-0.7579419840043.546810604170.01534438069730.9010317865780.0644717028828-0.3629387132420.9309658921610.6688751795090.0969247296005-0.697974763338-0.723725919310.1394611316320.04915768552660.829621724720.0313671898675-0.2239387346360.0958727339968-0.02886614578430.758239824376-18.760301223758.85540059229.63946072616
190.631357226249-0.443538256396-0.137675322991.53871235706-0.4843420653941.178705183770.05215353781870.1431935686340.792075953978-0.100491293958-0.06507593406210.124368761175-0.656437129799-0.0693778835981-0.2521302838040.854589616819-0.000102194677873-0.0679868721127-0.1820864266490.1091573816810.746861542837-33.516917520264.78454641765.9308788114
201.692753995780.337276753089-0.7562844660955.582903671941.155630801411.368549097540.1318158778950.01122377323070.400640984260.282103871758-0.105633437241-0.147202603744-0.4525067786040.105571217011-0.03464023178780.8737013031280.0506951688364-0.0617450703820.1228333926220.03969449140710.903436320679-24.395206077264.57458934329.75422795893
214.77008179934-1.552180211341.029264275643.07484184499-3.820027918385.770641584060.03518990954661.058671413621.50238401117-1.04135053891-0.0391173312475-0.107856879885-0.849164241833-0.05102783901040.08625341560790.7949968442070.0161537088172-0.03014133940680.3043155806980.1448558540180.615143629208-32.37317013163.4362295432-6.95116205756
224.579996829133.659357132991.993290737713.616231584231.15605004957.40812222537-0.3005624970730.5083584661380.313232636594-0.8011488494520.372977754229-0.258506073596-0.09579656601110.229633873202-0.1224142955360.622087546737-0.03712872514160.05495452158360.1486040567390.08532902989180.641257647353-26.550505237551.5354647424-11.0926570564
231.65816028434-0.712734150497-0.203040935971.59660940536-1.232943181051.37770379481-0.04203552825410.117215075888-0.426837693261-0.160123304022-0.1302410328410.01809133532810.657365978638-0.03198570127950.06056020580560.6745226362920.05938265634440.0854565007130.1109728837920.003631067214530.401401079316-30.854941933242.3263007256-1.16080502282
242.81894054258-0.279527869255-1.147508019673.09581569326-1.336651663465.13989419339-0.1332453239180.3503928391750.225014240972-0.062038537875-0.1304236142860.352825298039-0.266673686499-0.5080264141380.04335071854590.4867186033270.102144232254-0.02183711120150.09931896995170.10366989840.663505673466-40.895462325653.39576874112.34128973587
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 153 through 218 )
2X-RAY DIFFRACTION2chain 'A' and (resid 219 through 318 )
3X-RAY DIFFRACTION3chain 'A' and (resid 319 through 369 )
4X-RAY DIFFRACTION4chain 'A' and (resid 370 through 393 )
5X-RAY DIFFRACTION5chain 'A' and (resid 394 through 450 )
6X-RAY DIFFRACTION6chain 'B' and (resid 152 through 173 )
7X-RAY DIFFRACTION7chain 'B' and (resid 174 through 201 )
8X-RAY DIFFRACTION8chain 'B' and (resid 202 through 218 )
9X-RAY DIFFRACTION9chain 'B' and (resid 219 through 248 )
10X-RAY DIFFRACTION10chain 'B' and (resid 249 through 300 )
11X-RAY DIFFRACTION11chain 'B' and (resid 301 through 329 )
12X-RAY DIFFRACTION12chain 'B' and (resid 330 through 368 )
13X-RAY DIFFRACTION13chain 'B' and (resid 369 through 393 )
14X-RAY DIFFRACTION14chain 'B' and (resid 394 through 435 )
15X-RAY DIFFRACTION15chain 'B' and (resid 436 through 452 )
16X-RAY DIFFRACTION16chain 'C' and (resid 179 through 218 )
17X-RAY DIFFRACTION17chain 'C' and (resid 219 through 238 )
18X-RAY DIFFRACTION18chain 'C' and (resid 239 through 263 )
19X-RAY DIFFRACTION19chain 'C' and (resid 264 through 301 )
20X-RAY DIFFRACTION20chain 'C' and (resid 302 through 337 )
21X-RAY DIFFRACTION21chain 'C' and (resid 338 through 369 )
22X-RAY DIFFRACTION22chain 'C' and (resid 370 through 393 )
23X-RAY DIFFRACTION23chain 'C' and (resid 394 through 411 )
24X-RAY DIFFRACTION24chain 'C' and (resid 412 through 454 )

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