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- PDB-6n4o: Human Argonaute2-miR-122 bound to a seed and supplementary paired... -

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Basic information

Entry
Database: PDB / ID: 6n4o
TitleHuman Argonaute2-miR-122 bound to a seed and supplementary paired target
Components
  • Protein argonaute-2
  • RNA (5'-R(*CP*CP*AP*UP*UP*GP*UP*CP*AP*CP*AP*CP*UP*CP*CP*AP*AP*A)-3')
  • RNA (5'-R(P*UP*GP*GP*AP*GP*UP*GP*UP*GP*AP*CP*AP*AP*UP*GP*GP*UP*GP*UP*UP*U)-3')
KeywordsRNA binding protein/rna / RNA-binding protein / microRNA / target directed microRNA decay / HYDROLASE-RNA complex / RNA BINDING PROTEIN / RNA binding protein-rna complex
Function / homology
Function and homology information


: / endoribonuclease activity, cleaving miRNA-paired mRNA / endoribonuclease activity, cleaving siRNA-paired mRNA / siRNA-mediated gene silencing by mRNA destabilization / miRNA-mediated gene silencing by mRNA destabilization / Post-transcriptional silencing by small RNAs / Competing endogenous RNAs (ceRNAs) regulate PTEN translation / Regulation of CDH11 mRNA translation by microRNAs / Regulation of NPAS4 mRNA translation / Regulation of PTEN mRNA translation ...: / endoribonuclease activity, cleaving miRNA-paired mRNA / endoribonuclease activity, cleaving siRNA-paired mRNA / siRNA-mediated gene silencing by mRNA destabilization / miRNA-mediated gene silencing by mRNA destabilization / Post-transcriptional silencing by small RNAs / Competing endogenous RNAs (ceRNAs) regulate PTEN translation / Regulation of CDH11 mRNA translation by microRNAs / Regulation of NPAS4 mRNA translation / Regulation of PTEN mRNA translation / negative regulation of amyloid precursor protein biosynthetic process / Small interfering RNA (siRNA) biogenesis / positive regulation of trophoblast cell migration / Transcriptional Regulation by MECP2 / miRNA metabolic process / RISC-loading complex / mRNA cap binding / regulatory ncRNA-mediated post-transcriptional gene silencing / RISC complex assembly / miRNA processing / miRNA-mediated gene silencing by inhibition of translation / pre-miRNA processing / RNA 7-methylguanosine cap binding / siRNA processing / regulation of synapse maturation / siRNA binding / Regulation of MITF-M-dependent genes involved in apoptosis / mRNA 3'-UTR AU-rich region binding / M-decay: degradation of maternal mRNAs by maternally stored factors / RISC complex / regulatory ncRNA-mediated gene silencing / TGFBR3 expression / Regulation of RUNX1 Expression and Activity / P-body assembly / miRNA binding / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / MicroRNA (miRNA) biogenesis / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / RNA polymerase II complex binding / Regulation of MECP2 expression and activity / core promoter sequence-specific DNA binding / Nuclear events stimulated by ALK signaling in cancer / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / negative regulation of translational initiation / translation initiation factor activity / RNA endonuclease activity / post-embryonic development / positive regulation of translation / TP53 Regulates Metabolic Genes / Transcriptional regulation by small RNAs / P-body / MAPK6/MAPK4 signaling / Pre-NOTCH Transcription and Translation / cytoplasmic ribonucleoprotein granule / positive regulation of angiogenesis / double-stranded RNA binding / Ca2+ pathway / Estrogen-dependent gene expression / single-stranded RNA binding / postsynapse / translation / dendrite / glutamatergic synapse / positive regulation of transcription by RNA polymerase II / RNA binding / extracellular exosome / nucleoplasm / metal ion binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
Protein argonaute-2 / paz domain / Protein argonaute, Mid domain / Mid domain of argonaute / Argonaute linker 2 domain / Protein argonaute, N-terminal / Argonaute-like, PIWI domain / N-terminal domain of argonaute / Argonaute linker 2 domain / paz domain ...Protein argonaute-2 / paz domain / Protein argonaute, Mid domain / Mid domain of argonaute / Argonaute linker 2 domain / Protein argonaute, N-terminal / Argonaute-like, PIWI domain / N-terminal domain of argonaute / Argonaute linker 2 domain / paz domain / DUF1785 / Argonaute, linker 1 domain / Argonaute linker 1 domain / Piwi domain profile. / Piwi domain / Piwi domain / Piwi / PAZ domain superfamily / PAZ / PAZ domain / PAZ domain profile. / PAZ domain / Response regulator / Ribonuclease H-like superfamily/Ribonuclease H / Beta Complex / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / Protein argonaute-2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.899 Å
AuthorsSheu-Gruttadauria, J. / MacRae, I.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM104475 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM115649 United States
CitationJournal: Embo J. / Year: 2019
Title: Beyond the seed: structural basis for supplementary microRNA targeting by human Argonaute2.
Authors: Sheu-Gruttadauria, J. / Xiao, Y. / Gebert, L.F. / MacRae, I.J.
History
DepositionNov 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein argonaute-2
C: RNA (5'-R(P*UP*GP*GP*AP*GP*UP*GP*UP*GP*AP*CP*AP*AP*UP*GP*GP*UP*GP*UP*UP*U)-3')
D: RNA (5'-R(*CP*CP*AP*UP*UP*GP*UP*CP*AP*CP*AP*CP*UP*CP*CP*AP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)109,7833
Polymers109,7833
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7480 Å2
ΔGint-71 kcal/mol
Surface area38760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.132, 66.328, 247.677
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protein argonaute-2 / hAgo2 / Argonaute RISC catalytic component 2 / Eukaryotic translation initiation factor 2C 2 / ...hAgo2 / Argonaute RISC catalytic component 2 / Eukaryotic translation initiation factor 2C 2 / eIF2C 2 / PAZ Piwi domain protein / PPD / Protein slicer


Mass: 97358.188 Da / Num. of mol.: 1 / Mutation: D669A, S387D, S824A, S828D, S831D, S834A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AGO2, EIF2C2 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9UKV8, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters
#2: RNA chain RNA (5'-R(P*UP*GP*GP*AP*GP*UP*GP*UP*GP*AP*CP*AP*AP*UP*GP*GP*UP*GP*UP*UP*U)-3')


Mass: 6788.021 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: miR-122 21mer / Source: (synth.) Homo sapiens (human)
#3: RNA chain RNA (5'-R(*CP*CP*AP*UP*UP*GP*UP*CP*AP*CP*AP*CP*UP*CP*CP*AP*AP*A)-3')


Mass: 5636.419 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: 2.47 Å3/Da / Density % sol: 50.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 26% MPD, 5% PEG 3350, 50 mM imidazole pH 8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.88557 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.88557 Å / Relative weight: 1
ReflectionResolution: 2.89→39 Å / Num. obs: 24197 / % possible obs: 96.8 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.044 / Net I/σ(I): 13.5
Reflection shellResolution: 2.89→3.06 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.505 / Mean I/σ(I) obs: 4 / Rpim(I) all: 0.213 / % possible all: 96.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4W5O

4w5o


Resolution: 2.899→39 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.07
RfactorNum. reflection% reflection
Rfree0.2573 1236 5.12 %
Rwork0.2073 --
obs0.2099 24133 96.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.899→39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6384 680 0 0 7064
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037287
X-RAY DIFFRACTIONf_angle_d0.68410006
X-RAY DIFFRACTIONf_dihedral_angle_d13.6132835
X-RAY DIFFRACTIONf_chiral_restr0.0251142
X-RAY DIFFRACTIONf_plane_restr0.0031171
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8991-3.01520.32241330.28712474X-RAY DIFFRACTION95
3.0152-3.15240.32761340.26532543X-RAY DIFFRACTION98
3.1524-3.31850.30841310.23982523X-RAY DIFFRACTION97
3.3185-3.52630.29741260.23792434X-RAY DIFFRACTION94
3.5263-3.79830.2831450.21822571X-RAY DIFFRACTION99
3.7983-4.18020.23341430.18862556X-RAY DIFFRACTION98
4.1802-4.78420.22441280.1742536X-RAY DIFFRACTION95
4.7842-6.02420.26161340.192633X-RAY DIFFRACTION98
6.0242-39.65030.21851620.19542627X-RAY DIFFRACTION94
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)
12.47490.1037-0.65068.873-1.76088.516-0.0767-1.0521.0143-0.30480.2939-0.1101-0.8273-0.1494-0.25390.50130.0045-0.05290.4611-0.15250.4525-18.873430.1778-9.6827
25.8927-0.42461.34070.9749-0.33291.2599-0.3436-1.1895-0.148-0.01530.3084-0.14560.16380.05370.0620.409-0.02520.08250.6553-0.05470.2379-14.012611.2183-7.347
33.12820.31632.3462.35431.39742.3467-0.62471.9486-0.0174-1.7192-0.0987-1.1028-0.00021.50040.3591.21520.14730.35381.5130.06010.575214.23565.8984-25.1837
44.7079-1.05744.56696.1518-1.77834.68-0.13321.4149-1.2366-0.02030.09090.29290.6231-0.2884-0.27090.4041-0.07120.14890.94-0.27650.665511.7906-2.0809-14.8228
53.6881.8309-4.90585.6431-6.02979.25880.1245-0.7143-0.19451.47460.3650.6750.2158-0.4032-0.4621.19630.0959-0.1571.1186-0.18980.491111.85120.2217-3.3114
61.52630.1619-0.48935.1785.09845.9911-0.3267-0.1563-0.0478-0.11860.1308-0.06390.1538-0.0936-0.10140.2925-0.19370.0480.98-0.50290.42355.33243.8544-12.3195
73.7259-1.0821-2.31584.02362.5612.9745-0.5879-0.1886-0.258-0.41270.2577-0.156-0.0923-0.33260.42030.2058-0.154-0.01190.7691-0.03550.51158.48248.7942-10.3049
86.3788-1.4931-0.4691.4644-0.05562.1795-0.3111-0.74640.50270.32340.0175-0.395-0.2865-0.3034-0.2041-0.29190.2135-0.01911.3408-0.45640.692119.364313.9434-8.056
94.9184-0.2913-0.49393.20194.84477.3568-0.1983-0.0158-0.3931-0.41950.5224-0.6506-0.20750.9377-0.30930.48540.0392-0.0260.85920.13760.69919.7444-0.7172-17.336
102.1231-0.6734-0.5134.79760.57962.95030.02411.1267-0.0405-1.2358-0.20280.0951-0.5183-0.1311-0.01770.5284-0.11120.09250.9468-0.30880.28314.29599.0279-14.3052
114.0395-4.9025-0.2556.31020.31360.0166-0.3775-1.65650.94730.9370.6512-0.43530.05020.0266-0.11220.24810.1862-0.01620.8376-0.22960.4717-7.343418.8411-1.3547
123.7504-1.4178-3.1994.01943.93194.9579-0.3512-0.048-0.2519-0.24320.7067-0.4912-0.18590.228-0.32750.4273-0.0352-0.06110.7384-0.02180.3339-4.89647.0389-15.1517
132.97250.2477-1.06932.33291.78714.98520.16971.0229-0.6167-0.1045-0.459-0.30880.5943-0.86480.33210.37520.01370.05310.8403-0.20070.5706-12.00250.4157-23.4629
145.40953.75090.58972.81321.34328.3151-1.1015-0.7743-1.3242-0.4378-0.29141.08371.2162-1.72251.15440.8896-0.12640.15911.661-0.38281.1644-5.2871-14.2918-45.4388
159.064.522-2.10143.2726-3.98138.9899-1.7324-0.21810.0561-1.85840.51070.87371.5904-0.70640.95461.26890.02420.02291.6281-0.75891.4261-8.8484-19.9837-51.2746
167.25126.0605-0.00597.0746-0.62310.18550.83321.11410.4995-3.2531-0.06960.25540.2225-0.3664-0.4151.73450.68470.29241.6079-0.06630.7781-1.7547-6.997-52.759
178.4829-5.47616.11658.4272-4.50484.49490.6428-0.37140.1859-0.6194-0.7049-0.35390.8895-0.00790.0491.29280.38260.50240.99620.0840.9776.7763-12.2046-37.8326
181.3041.17640.75484.40111.1652.899-0.45930.44852.41230.24590.1673-0.3655-0.01561.82920.27260.73060.08020.28781.293-0.16771.737910.6298-9.6671-35.0221
194.6101-3.58080.53184.92742.02232.8226-1.71020.4358-0.2081-1.3044-0.0365-1.30380.82290.9521.53390.92240.020.13251.05610.01920.71227.2873-6.2572-48.2741
200.7195-0.94020.43658.827-1.26180.33560.37220.3971-0.204-1.0934-0.02150.4081-0.00121.9626-0.42531.36350.39940.54361.5604-0.07741.303913.7597-14.2889-55.0326
212.1833-1.0699-0.82654.4617-0.8340.70550.292-0.00851.1778-0.7988-0.7705-1.8642-0.08130.5990.21231.20820.29870.90991.03750.60732.020622.787-16.994-53.083
220.8864-2.08481.47976.45-0.34998.11811.0014-0.06090.9675-1.9959-0.5809-0.82372.40310.25730.47581.830.54050.37351.2187-0.18310.938811.8345-23.7518-47.1699
235.26625.04495.87997.11986.04566.63-0.38960.9314-0.37410.52511.4444-1.12510.27180.7314-0.99861.44150.12220.38611.5916-0.25910.683210.4706-8.5499-46.5503
245.5077-1.6779-3.66250.95731.04812.0424-0.48221.919-0.9345-0.5109-0.21510.08760.4294-0.29010.53430.74580.00120.04681.2153-0.10210.6953-10.112-5.3818-33.1534
251.2059-0.32560.64620.8982-0.39562.82310.1095-0.07920.0117-0.3633-0.03570.14190.0737-0.1896-0.08270.4052-0.0386-0.00110.1432-0.04950.379-34.138318.7649-43.7072
261.58820.2890.16151.3288-0.19962.6906-0.0915-0.25190.2926-0.0890.0235-0.102-0.52690.19490.08710.3439-0.0135-0.00430.3139-0.08060.3662-24.249327.5884-26.7893
273.2302-0.86892.52131.0505-1.07932.18070.44790.41450.3372-0.3243-0.94090.2742-1.4655-1.27720.31971.616-0.1270.7610.9262-0.29560.9952-7.034833.907-48.0132
287.8714-2.37050.45083.05962.31582.58790.541-1.502-0.2639-0.3932-0.3981-0.8644-1.61860.93220.01950.5691-0.21520.0970.9047-0.09280.4856-15.290834.1525-47.7682
291.9598-2.84081.38517.4984-3.46342.0094-0.148-0.15071.28160.54110.8357-0.6752-0.9144-0.1875-0.42750.73710.00160.08740.2811-0.11810.6172-26.021337.7035-49.2697
302.5911-3.0986-1.78245.1905-0.82319.00520.1456-0.55210.9633-1.08640.17560.4187-1.1733-0.36370.16830.6592-0.04280.06880.4981-0.08610.3083-28.8832.2571-42.8622
311.2063-1.0033-0.09955.2285-4.10294.12380.1205-0.2331-0.2921-0.2812-0.0794-0.50880.64641.1127-0.05520.49310.0786-0.07050.412-0.0140.5068-25.882710.5722-37.0874
325.0991-2.9583-5.46345.48814.82866.56820.01850.49193.1387-0.46940.7272-0.7239-0.1874-0.6251-0.98081.394-0.0037-0.08321.74010.1861.99585.17714.4488-34.1815
339.1705-2.63571.91512.8796-2.35372.0927-0.7959-0.47821.03440.4657-0.3532-1.5029-1.05920.40071.09141.3670.00630.08081.8444-0.24872.325719.3584-13.8743-41.0705
340.3406-0.69960.33692.7482-0.74083.84630.4994-0.7770.44120.15440.7242-0.7021.01481.1465-1.32391.33960.0182-0.35822.9042-0.24291.2134.48138.672-42.5501
353.5068-0.5185-3.38647.3946-1.34413.7981-0.09550.715-0.69410.07350.28190.2047-0.6148-0.4124-0.38320.7878-0.036-0.17460.5396-0.08330.679-29.95176.1612-39.2964
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 22 through 31 )
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 58 )
3X-RAY DIFFRACTION3chain 'A' and (resid 59 through 67 )
4X-RAY DIFFRACTION4chain 'A' and (resid 68 through 85 )
5X-RAY DIFFRACTION5chain 'A' and (resid 86 through 90 )
6X-RAY DIFFRACTION6chain 'A' and (resid 91 through 95 )
7X-RAY DIFFRACTION7chain 'A' and (resid 96 through 107 )
8X-RAY DIFFRACTION8chain 'A' and (resid 108 through 112 )
9X-RAY DIFFRACTION9chain 'A' and (resid 113 through 120 )
10X-RAY DIFFRACTION10chain 'A' and (resid 126 through 139 )
11X-RAY DIFFRACTION11chain 'A' and (resid 140 through 148 )
12X-RAY DIFFRACTION12chain 'A' and (resid 149 through 185 )
13X-RAY DIFFRACTION13chain 'A' and (resid 190 through 229 )
14X-RAY DIFFRACTION14chain 'A' and (resid 230 through 238 )
15X-RAY DIFFRACTION15chain 'A' and (resid 239 through 246 )
16X-RAY DIFFRACTION16chain 'A' and (resid 251 through 262 )
17X-RAY DIFFRACTION17chain 'A' and (resid 263 through 272 )
18X-RAY DIFFRACTION18chain 'A' and (resid 276 through 280 )
19X-RAY DIFFRACTION19chain 'A' and (resid 281 through 285 )
20X-RAY DIFFRACTION20chain 'A' and (resid 286 through 295 )
21X-RAY DIFFRACTION21chain 'A' and (resid 303 through 307 )
22X-RAY DIFFRACTION22chain 'A' and (resid 308 through 325 )
23X-RAY DIFFRACTION23chain 'A' and (resid 326 through 332 )
24X-RAY DIFFRACTION24chain 'A' and (resid 334 through 384 )
25X-RAY DIFFRACTION25chain 'A' and (resid 385 through 571 )
26X-RAY DIFFRACTION26chain 'A' and (resid 572 through 819 )
27X-RAY DIFFRACTION27chain 'A' and (resid 838 through 842 )
28X-RAY DIFFRACTION28chain 'A' and (resid 843 through 847 )
29X-RAY DIFFRACTION29chain 'A' and (resid 848 through 852 )
30X-RAY DIFFRACTION30chain 'A' and (resid 853 through 859 )
31X-RAY DIFFRACTION31chain 'C' and (resid 1 through 9 )
32X-RAY DIFFRACTION32chain 'C' and (resid 11 through 18 )
33X-RAY DIFFRACTION33chain 'C' and (resid 20 through 21 )
34X-RAY DIFFRACTION34chain 'D' and (resid 1 through 6 )
35X-RAY DIFFRACTION35chain 'D' and (resid 9 through 16 )

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