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- PDB-7o56: X-ray Structure of Interferon Regulatory Factor 4 DNA binding dom... -

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Basic information

Entry
Database: PDB / ID: 7o56
TitleX-ray Structure of Interferon Regulatory Factor 4 DNA binding domain bound to an interferon-stimulated response element solved by Phosphorus and Sulphur SAD methods
Components
  • DNA (5'-D(P*AP*AP*TP*AP*AP*AP*AP*GP*AP*AP*AP*CP*CP*GP*AP*AP*AP*GP*TP*AP*A)-3')
  • DNA (5'-D(P*TP*TP*TP*AP*CP*TP*TP*TP*CP*GP*GP*TP*TP*TP*CP*TP*TP*TP*TP*AP*T)-3')
  • Interferon regulatory factor 4Interferon regulatory factors
KeywordsDNA BINDING PROTEIN / INTERFERON REGULATORY FACTORS / TRANSCRIPTION REGULATION / PROTEIN-DNA INTERACTION / TRANSCRIPTION
Function / homology
Function and homology information


negative regulation of toll-like receptor signaling pathway / T-helper 17 cell lineage commitment / regulation of T-helper cell differentiation / myeloid dendritic cell differentiation / positive regulation of interleukin-13 production / immune system process / defense response to protozoan / positive regulation of interleukin-10 production / positive regulation of interleukin-4 production / positive regulation of interleukin-2 production ...negative regulation of toll-like receptor signaling pathway / T-helper 17 cell lineage commitment / regulation of T-helper cell differentiation / myeloid dendritic cell differentiation / positive regulation of interleukin-13 production / immune system process / defense response to protozoan / positive regulation of interleukin-10 production / positive regulation of interleukin-4 production / positive regulation of interleukin-2 production / T cell activation / Interferon gamma signaling / nucleosome / Interferon alpha/beta signaling / sequence-specific double-stranded DNA binding / positive regulation of cold-induced thermogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / Interleukin-4 and Interleukin-13 signaling / sequence-specific DNA binding / transcription coactivator activity / DNA-binding transcription factor activity, RNA polymerase II-specific / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / nucleoplasm / membrane / nucleus / cytosol
Similarity search - Function
Interferon regulatory factor-3 / Interferon-regulatory factor 3 / Interferon-regulatory factor 3 / Interferon regulatory factor, conserved site / IRF tryptophan pentad repeat DNA-binding domain signature. / Interferon regulatory factor transcription factor / interferon regulatory factor / IRF tryptophan pentad repeat DNA-binding domain profile. / Interferon regulatory factor DNA-binding domain / SMAD-like domain superfamily ...Interferon regulatory factor-3 / Interferon-regulatory factor 3 / Interferon-regulatory factor 3 / Interferon regulatory factor, conserved site / IRF tryptophan pentad repeat DNA-binding domain signature. / Interferon regulatory factor transcription factor / interferon regulatory factor / IRF tryptophan pentad repeat DNA-binding domain profile. / Interferon regulatory factor DNA-binding domain / SMAD-like domain superfamily / SMAD/FHA domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Interferon regulatory factor 4
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsEl Omari, K. / Agnarelli, A. / Duman, R. / Wagner, A. / Mancini, E.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust204833/Z/16/Z United Kingdom
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2021
Title: Phosphorus and sulfur SAD phasing of the nucleic acid-bound DNA-binding domain of interferon regulatory factor 4.
Authors: Agnarelli, A. / El Omari, K. / Duman, R. / Wagner, A. / Mancini, E.J.
History
DepositionApr 7, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 13, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / diffrn_source / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_seq_map_depositor_info.one_letter_code_mod

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interferon regulatory factor 4
D: DNA (5'-D(P*AP*AP*TP*AP*AP*AP*AP*GP*AP*AP*AP*CP*CP*GP*AP*AP*AP*GP*TP*AP*A)-3')
E: DNA (5'-D(P*TP*TP*TP*AP*CP*TP*TP*TP*CP*GP*GP*TP*TP*TP*CP*TP*TP*TP*TP*AP*T)-3')
B: Interferon regulatory factor 4
C: Interferon regulatory factor 4


Theoretical massNumber of molelcules
Total (without water)61,8005
Polymers61,8005
Non-polymers00
Water0
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)77.880, 112.440, 140.660
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 22 through 102 or resid 104 through 130))
d_2ens_1(chain "B" and (resid 22 through 102 or resid 104 through 130))
d_3ens_1(chain "C" and (resid 22 through 102 or resid 104 through 130))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLYASNA2 - 82
d_12ens_1SERGLUA84 - 110
d_21ens_1GLYASND1 - 81
d_22ens_1SERGLUD83 - 109
d_31ens_1GLYASNE4 - 84
d_32ens_1SERGLUE86 - 112

NCS oper:
IDCodeMatrixVector
1given(-0.394597010314, 0.837441651588, -0.378133150671), (0.831574923571, 0.500531120979, 0.240731683455), (0.390866148367, -0.21945404329, -0.893903561322)-63.797458965, 62.0550867748, -155.554115216
2given(-0.0735725878509, 0.793842736131, 0.603656180792), (0.501663481526, 0.552599363976, -0.665558182458), (-0.861928550183, 0.253865423452, -0.438898076044)48.421124404, -8.25939769158, -153.861064753

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Components

#1: Protein Interferon regulatory factor 4 / Interferon regulatory factors / IRF-4 / Lymphocyte-specific interferon regulatory factor / LSIRF / Multiple myeloma oncogene 1 / NF-EM5


Mass: 16306.470 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IRF4, MUM1 / Plasmid: pCDFDuet / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q15306
#2: DNA chain DNA (5'-D(P*AP*AP*TP*AP*AP*AP*AP*GP*AP*AP*AP*CP*CP*GP*AP*AP*AP*GP*TP*AP*A)-3')


Mass: 6514.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*TP*TP*TP*AP*CP*TP*TP*TP*CP*GP*GP*TP*TP*TP*CP*TP*TP*TP*TP*AP*T)-3')


Mass: 6366.112 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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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: 2.49 Å3/Da / Density % sol: 50.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.2 / Details: 0.1M sodium acetate, 5% PEG 4000, 10mM EDTA

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: DIAMOND / Beamline: I23 / Wavelength: 2.7552 Å
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: May 14, 2019
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.7552 Å / Relative weight: 1
ReflectionResolution: 2.6→70.33 Å / Num. obs: 19282 / % possible obs: 99.24 % / Redundancy: 81 % / Biso Wilson estimate: 79.26 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.103 / Rrim(I) all: 0.104 / Net I/σ(I): 41.49
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 66.1 % / Rmerge(I) obs: 2.76 / Mean I/σ(I) obs: 1.65 / Num. unique obs: 1865 / CC1/2: 0.75 / Rrim(I) all: 2.781 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874refinement
XDSdata reduction
XSCALEdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→70.33 Å / SU ML: 0.4259 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.6508
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2413 910 4.72 %
Rwork0.2121 18356 -
obs0.2136 19266 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 115.84 Å2
Refinement stepCycle: LAST / Resolution: 2.6→70.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2805 861 0 0 3666
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00993847
X-RAY DIFFRACTIONf_angle_d1.2395371
X-RAY DIFFRACTIONf_chiral_restr0.06548
X-RAY DIFFRACTIONf_plane_restr0.0082547
X-RAY DIFFRACTIONf_dihedral_angle_d25.06031523
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.600860274846
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.574741570467
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.730.39391190.37042563X-RAY DIFFRACTION98.21
2.74-2.910.36111280.32172557X-RAY DIFFRACTION99
2.91-3.130.35121170.30982641X-RAY DIFFRACTION99.71
3.13-3.450.3161250.23932550X-RAY DIFFRACTION97.73
3.45-3.940.25981340.21662625X-RAY DIFFRACTION100
3.94-4.970.21821350.19412661X-RAY DIFFRACTION100
4.97-70.330.19411520.17092759X-RAY DIFFRACTION99.9
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)
15.600512836785.907641588943.056510732966.966047689913.115671401431.685978847790.513275440585-0.3500806615750.9230803062140.366647990233-0.1414605457160.0259760973441-2.03114687815-1.269425098940.4298768790370.8778260462620.3370090819170.02054447174121.13083439095-0.0273276332890.618474103561-49.34476216116.66872866648-87.9419122472
22.712604306021.571038208451.884528392854.15503209277-2.168099658144.58211442822-0.218721740615-0.1659485220950.4086876731520.8191114614820.2494783609381.18906358185-0.975804107998-0.5875442480780.5821944714150.7338632238810.2653634378880.07276650226512.058168825280.01966652849950.810653666499-58.97555130962.76973336298-82.8843092888
30.421323276982-0.216035819145-0.6233676934180.7427718316630.1034454251890.9984588037220.007199382770820.257126299086-0.29945882372-0.00663599895672-0.2970146578870.383696513972-0.0188953363901-0.535804542684-0.08030749145850.514592874211-0.1228419209710.1064403357581.59709044160.1026234753860.660947299107-55.538300032-2.82602062592-81.1182356849
42.82718938931-0.658846916884-1.162311926693.68649673473-4.457326140366.801855518120.131122088957-0.0351850743316-0.1751441870990.385092279271-0.543821041770.1646215055560.37879710468-1.70125737449-0.2247856684430.600084116538-0.3374485744790.1174612806831.23499604014-0.1129820436580.548960451891-53.3621916001-9.65985773613-93.5059071093
51.50059782524-3.16505346075-3.3154009466.803580115717.39195024158.593688260840.1987900914331.15036046802-0.181714969734-0.196278165912-0.540679167179-0.5276347594870.1203873582-0.3699634808450.3742864209570.4852053984160.009606594641280.01406580491040.7122618524810.05149696101020.541494431995-43.9516554227-4.74440966624-104.074089709
62.83162849667-0.181328730322-1.798589520750.928763366032-0.4046377943751.52989145870.262894023817-0.848945277228-0.06153702765450.707008055972-0.1771029150310.09068399771970.164511678564-1.45919786940.6337299405730.617685859623-0.2167079403980.0009002106609351.050488863530.01950660452510.500338444378-48.7572677427-6.38237734339-82.2094083817
73.28279932393-1.33158390732.366376457274.444647611382.594347105687.274494312040.0506127569025-0.0536604046423-0.0922635884880.0241562215799-0.859509458390.6080874693021.18463516572-3.35938355667-0.2413350571361.010365327480.178689319955-0.05511165423570.949408667542-0.3460454762520.212330182375-41.270412259112.9166443907-72.9142841274
82.902111460960.5427533498740.1535326050871.83195343358-0.8184085969933.161423206880.383197972509-0.439434739525-1.47074099299-0.544658782493-0.184553326642-0.7747047092311.960689671780.0274586663249-0.5135827076931.19799029013-0.469777545866-0.06580886469290.7106317114630.09152272222110.913113263885-41.4463270899-20.652502786-88.4274031485
93.055638668220.4734823144540.8906793571383.5545475361.053108800043.17017510735-0.114814982212-0.3927916736871.466142958850.121629652637-0.287204741705-0.782859247395-2.005512453941.36727833703-0.4909359258290.919606541381-0.939428429112-0.3745993529780.651892472296-0.06672564095750.790469376611-23.54541065748.46527057207-88.9358133699
103.728221701791.552018062760.07704470953070.6864042756790.3637485377922.53030313573-0.05875147669290.4181061409151.17749748645-0.134875201480.0112484081761-0.483543902588-1.389599717011.055162701730.2145492258131.2478911193-0.848069055961-0.2223643628721.19862007490.1391365183931.15965986673-20.194708831412.633097107-89.6066544256
112.913756283321.458366082631.245718900052.94995135358-0.6337731496954.055417395810.455951767317-0.449874354594-0.7401312101530.61049590662-0.6413039709240.1338381132141.32509663425-0.4020038824-0.4209020183310.864694839403-0.2392143415290.0654383035090.5777753558620.00335952053420.696716724884-38.7261976634-15.8092203062-87.9364830068
124.978486450510.7468485737760.4416802513041.37564675109-0.1034653765340.492362754959-0.1304108810660.663968670117-0.191154119172-0.2351875731270.105300704812-0.357355024665-0.1847866145420.6975911774480.09396931991170.468951867412-0.4611445035670.003033023715142.770670026750.08435919972050.982532004414-5.559094172662.36536640434-97.9108184427
131.55521530969-1.076908958490.09210484565610.9461578412760.5324140812891.81061542103-0.03027453168561.597283404590.365595296134-0.4240995148450.124716765245-0.6941803043690.175128482652.200288460170.9502477566330.4425309572210.1297255622450.003758219040832.17003392967-0.05174843734840.795892704234-12.9893725886-8.48442728654-100.683331331
147.68158500262-0.7583217010871.436232607423.775784264651.456459956943.92929640641-0.04447861380030.965431097986-0.4904244228710.243184111502-0.0246892109093-0.532258233363-0.2006061586931.68630374926-0.6107527752130.489861529544-0.1292404765-0.1520016993031.917504120210.008381644160870.860808478134-11.1623783256-6.35594650573-88.8670854306
152.117424104581.07233896286-3.146194942578.64456838208-1.43235863874.67899494342-0.304727156982-0.07452329685860.3194405720321.09484890928-0.0050013537322-0.524925746947-0.2582514874021.72021241637-0.03455781526460.902449737622-0.2459303069-0.2864143548231.964561604420.01919065948860.736679839272-10.9494651064-1.96103518866-78.9347338203
161.924275068240.08794887608112.372085886720.7743178934151.000452802896.041210895050.005362012497090.7748758444690.348926966451-0.0813378752007-0.1168161545680.025112902561-0.8429145262471.9871155318-0.001996545341080.372342245411-0.226997755112-0.08183868386841.481398568850.05037268267620.561661517485-19.4515212587-1.49079345351-98.5588367441
175.369147896512.267187963691.474698277152.870345460231.620000399161.65256963304-0.7513527595341.776281478690.570334514004-0.8551294405451.027987184560.114629540607-0.3863687567280.9086531702220.3808916740910.445239270881-0.375166017389-0.07180074905582.159620235030.1342476915640.72083470807-14.42053335972.07667671396-105.984262115
182.50860857231.30089699527-2.093869904260.674339201798-1.085271226251.74663760680.703605462631-2.72072711963-2.182594237151.12781316949-2.18318655136-0.459052100731.309138991772.924422232591.364868238221.96934812765-0.0625412368706-0.5328878177211.281050151840.5101273304261.501884336391.9940760894435.6242198711-77.5887371689
191.15264636836-0.944961865683-0.7588958189463.808548618450.721042451.75548522313-0.664576077738-0.8892361673440.2533400480320.04313142346860.475874114934-0.673570692034-0.4327108465741.691537658140.2430513292372.49127658198-0.525659209279-0.7283411265171.826545245840.3375228339991.613836068354.5787770638122.3195093402-67.3265326799
206.65585279646-5.44168978182-5.849835778524.471141212224.779043162215.141136444660.259361592667-2.156322407760.3604434125010.32010672103-0.3321565962780.240146753393-0.2292462302850.913263952283-0.1021687973481.70090968668-0.577818005283-0.5039689652811.432072638990.3746388908522.042222271281.3084538575816.2352735807-71.0459498284
211.86752139053-0.5518796952752.205995291764.829574579113.553538215116.39309755125-0.179122332569-0.760030258835-0.2128958800260.6695138561540.03125560230580.6116614018540.17901070137-0.03198867555380.1525623862222.01165265863-0.415903799973-0.1533435779371.457230068990.3040009423071.20613215546-11.848901286121.8857014173-69.2054213106
228.98551919336-1.17871473105-0.5135944582310.55100442530.4576796312170.495424391804-0.400605710796-1.463005939890.3061560406310.05476649565950.647649116924-0.216057171431-0.8800437983120.9837837370470.3095395011512.66516792937-0.5569664783130.09108480814551.445571386680.1732986426261.16651993393-14.708741097836.3427067539-71.3326712682
231.26089233139-1.995355248450.1640799269863.652022949320.1277635606423.331672992310.154422479237-0.464775275229-0.3458798159330.347536046332-0.238530923446-0.3910919156830.480954855925-0.02416837151480.2651082786011.76331285306-0.196753708859-0.250417951471.302201670770.2113359009761.41747927474-3.7845980465718.9492679684-77.7538735398
242.026961079273.363822653170.04528005365967.547111623781.48316850091.43806717495-0.856616216641-0.435437334267-0.7796819807720.04178470831630.038406961156-1.196821201250.1168934282041.111177804580.9150610150671.71877068115-0.514988913729-0.3404650968961.381967402310.4077280555472.137552632425.7396372205718.4098397235-76.7770672813
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 21 through 33 )AA21 - 331 - 13
22chain 'A' and (resid 34 through 48 )AA34 - 4814 - 28
33chain 'A' and (resid 49 through 53 )AA49 - 5329 - 33
44chain 'A' and (resid 54 through 77 )AA54 - 7734 - 57
55chain 'A' and (resid 78 through 89 )AA78 - 8958 - 69
66chain 'A' and (resid 90 through 127 )AA90 - 12770 - 107
77chain 'A' and (resid 128 through 134 )AA128 - 134108 - 114
88chain 'D' and (resid 1 through 10 )DB1 - 10
99chain 'D' and (resid 11 through 21 )DB11 - 21
1010chain 'E' and (resid 1 through 10 )EC1 - 10
1111chain 'E' and (resid 11 through 21 )EC11 - 21
1212chain 'B' and (resid 22 through 33 )BD22 - 331 - 12
1313chain 'B' and (resid 34 through 63 )BD34 - 6313 - 42
1414chain 'B' and (resid 64 through 77 )BD64 - 7743 - 56
1515chain 'B' and (resid 78 through 89 )BD78 - 8957 - 68
1616chain 'B' and (resid 90 through 121 )BD90 - 12169 - 100
1717chain 'B' and (resid 122 through 130 )BD122 - 130101 - 109
1818chain 'C' and (resid 19 through 24 )CE19 - 241 - 6
1919chain 'C' and (resid 25 through 48 )CE25 - 487 - 30
2020chain 'C' and (resid 49 through 53 )CE49 - 5331 - 35
2121chain 'C' and (resid 54 through 77 )CE54 - 7736 - 59
2222chain 'C' and (resid 78 through 89 )CE78 - 8960 - 71
2323chain 'C' and (resid 90 through 121 )CE90 - 12172 - 103
2424chain 'C' and (resid 122 through 130 )CE122 - 130104 - 112

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