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- PDB-5nt1: Complex of influenza A NS1 effector domain with TRIM25 coiled coil -

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Basic information

Entry
Database: PDB / ID: 5nt1
TitleComplex of influenza A NS1 effector domain with TRIM25 coiled coil
Components
  • E3 ubiquitin/ISG15 ligase TRIM25
  • Non-structural protein 1
KeywordsLIGASE / Viral protein/host protein
Function / homology
Function and homology information


: / Inhibition of IFN-beta / Inhibition of PKR / Inhibition of Host mRNA Processing and RNA Silencing / RIG-I binding / regulation of viral entry into host cell / symbiont-mediated suppression of host mRNA processing / suppression of viral release by host / Microbial modulation of RIPK1-mediated regulated necrosis / symbiont-mediated suppression of host PKR/eIFalpha signaling ...: / Inhibition of IFN-beta / Inhibition of PKR / Inhibition of Host mRNA Processing and RNA Silencing / RIG-I binding / regulation of viral entry into host cell / symbiont-mediated suppression of host mRNA processing / suppression of viral release by host / Microbial modulation of RIPK1-mediated regulated necrosis / symbiont-mediated suppression of host PKR/eIFalpha signaling / negative regulation of viral entry into host cell / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / response to vitamin D / NS1 Mediated Effects on Host Pathways / protein serine/threonine kinase inhibitor activity / ERAD pathway / RIPK1-mediated regulated necrosis / TRAF6 mediated IRF7 activation / cytoplasmic pattern recognition receptor signaling pathway / protein monoubiquitination / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / antiviral innate immune response / ligase activity / TRAF6 mediated NF-kB activation / Viral mRNA Translation / viral release from host cell / protein K48-linked ubiquitination / cellular response to leukemia inhibitory factor / Negative regulators of DDX58/IFIH1 signaling / Termination of translesion DNA synthesis / DDX58/IFIH1-mediated induction of interferon-alpha/beta / RING-type E3 ubiquitin transferase / PKR-mediated signaling / ISG15 antiviral mechanism / cytoplasmic stress granule / positive regulation of DNA-binding transcription factor activity / response to estrogen / ubiquitin-protein transferase activity / regulation of protein localization / SARS-CoV-1 activates/modulates innate immune responses / ubiquitin protein ligase activity / Interferon gamma signaling / Ovarian tumor domain proteases / positive regulation of NF-kappaB transcription factor activity / TRAF3-dependent IRF activation pathway / ubiquitin-dependent protein catabolic process / positive regulation of canonical NF-kappaB signal transduction / response to oxidative stress / host cell cytoplasm / transcription coactivator activity / nuclear body / cadherin binding / innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / RNA binding / nucleoplasm / identical protein binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
TRIM25, PRY/SPRY domain / Influenza virus non-structural protein, effector domain / Influenza A virus NS1 protein / Influenza A virus NS1, effector domain-like superfamily / Influenza non-structural protein (NS1) / Influenza non-structural protein (NS1) / Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / SPRY-associated domain / SPRY-associated ...TRIM25, PRY/SPRY domain / Influenza virus non-structural protein, effector domain / Influenza A virus NS1 protein / Influenza A virus NS1, effector domain-like superfamily / Influenza non-structural protein (NS1) / Influenza non-structural protein (NS1) / Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / SPRY domain / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / S15/NS1, RNA-binding / Nucleotidyltransferase; domain 5 / Concanavalin A-like lectin/glucanase domain superfamily / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Non-structural protein 1 / E3 ubiquitin/ISG15 ligase TRIM25
Similarity search - Component
Biological speciesHomo sapiens (human)
Influenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.82 Å
AuthorsKoliopoulos, M.G. / Rittinger, K.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
The Francis Crick InstituteFC001142 United Kingdom
CitationJournal: Nat Commun / Year: 2018
Title: Molecular mechanism of influenza A NS1-mediated TRIM25 recognition and inhibition.
Authors: Koliopoulos, M.G. / Lethier, M. / van der Veen, A.G. / Haubrich, K. / Hennig, J. / Kowalinski, E. / Stevens, R.V. / Martin, S.R. / Reis E Sousa, C. / Cusack, S. / Rittinger, K.
History
DepositionApr 27, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1May 23, 2018Group: Data collection / 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 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
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: E3 ubiquitin/ISG15 ligase TRIM25
B: Non-structural protein 1
E: E3 ubiquitin/ISG15 ligase TRIM25
F: Non-structural protein 1
I: E3 ubiquitin/ISG15 ligase TRIM25
J: Non-structural protein 1


Theoretical massNumber of molelcules
Total (without water)117,2906
Polymers117,2906
Non-polymers00
Water1448
1
A: E3 ubiquitin/ISG15 ligase TRIM25
B: Non-structural protein 1

A: E3 ubiquitin/ISG15 ligase TRIM25
B: Non-structural protein 1


Theoretical massNumber of molelcules
Total (without water)78,1934
Polymers78,1934
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
2
I: E3 ubiquitin/ISG15 ligase TRIM25
J: Non-structural protein 1

E: E3 ubiquitin/ISG15 ligase TRIM25
F: Non-structural protein 1


Theoretical massNumber of molelcules
Total (without water)78,1934
Polymers78,1934
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
3
E: E3 ubiquitin/ISG15 ligase TRIM25
F: Non-structural protein 1

I: E3 ubiquitin/ISG15 ligase TRIM25
J: Non-structural protein 1


Theoretical massNumber of molelcules
Total (without water)78,1934
Polymers78,1934
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Unit cell
Length a, b, c (Å)131.380, 225.230, 146.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222

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Components

#1: Protein E3 ubiquitin/ISG15 ligase TRIM25 / Estrogen-responsive finger protein / RING finger protein 147 / RING-type E3 ubiquitin transferase / ...Estrogen-responsive finger protein / RING finger protein 147 / RING-type E3 ubiquitin transferase / RING-type E3 ubiquitin transferase TRIM25 / Tripartite motif-containing protein 25 / Ubiquitin/ISG15-conjugating enzyme TRIM25 / Zinc finger protein 147


Mass: 22011.930 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM25, EFP, RNF147, ZNF147 / Production host: Escherichia coli (E. coli)
References: UniProt: Q14258, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases), RING-type E3 ubiquitin transferase
#2: Protein Non-structural protein 1 / NS1 / NS1A


Mass: 17084.688 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain A/Puerto Rico/8/1934 H1N1)
Strain: A/Puerto Rico/8/1934 H1N1 / Gene: NS / Production host: Escherichia coli (E. coli) / References: UniProt: P03496
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

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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: 4.62 Å3/Da / Density % sol: 73.36 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM Tris pH 8.5 25 % PEG 600 200 mM sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.82→48.68 Å / Num. obs: 52603 / % possible obs: 99.9 % / Redundancy: 6.8 % / CC1/2: 1 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.042 / Net I/σ(I): 14.9
Reflection shellResolution: 2.82→2.89 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 3878 / CC1/2: 0.6 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LTB

4ltb


Resolution: 2.82→48.685 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2244 2600 4.94 %
Rwork0.1949 --
obs0.1964 52584 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.82→48.685 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7030 0 0 8 7038
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067114
X-RAY DIFFRACTIONf_angle_d0.89568
X-RAY DIFFRACTIONf_dihedral_angle_d16.7344475
X-RAY DIFFRACTIONf_chiral_restr0.0471117
X-RAY DIFFRACTIONf_plane_restr0.0051220
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.82-2.87130.4071260.39422634X-RAY DIFFRACTION100
2.8713-2.92650.40681360.342594X-RAY DIFFRACTION100
2.9265-2.98620.40711640.30962570X-RAY DIFFRACTION100
2.9862-3.05120.36551100.27322637X-RAY DIFFRACTION100
3.0512-3.12210.28881230.26392601X-RAY DIFFRACTION100
3.1221-3.20020.3311210.25392612X-RAY DIFFRACTION100
3.2002-3.28670.27761470.24262598X-RAY DIFFRACTION100
3.2867-3.38340.2411960.22842654X-RAY DIFFRACTION100
3.3834-3.49260.25311310.23132619X-RAY DIFFRACTION100
3.4926-3.61740.25081370.20632616X-RAY DIFFRACTION100
3.6174-3.76210.22371460.19592617X-RAY DIFFRACTION100
3.7621-3.93330.25551390.17482620X-RAY DIFFRACTION100
3.9333-4.14060.19951370.16422611X-RAY DIFFRACTION100
4.1406-4.39980.20481450.15082636X-RAY DIFFRACTION100
4.3998-4.73930.19971280.15132644X-RAY DIFFRACTION100
4.7393-5.21570.18181560.15472632X-RAY DIFFRACTION100
5.2157-5.96930.23731460.19252664X-RAY DIFFRACTION100
5.9693-7.51620.22021630.2112655X-RAY DIFFRACTION100
7.5162-48.69210.15811490.1642770X-RAY DIFFRACTION99
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)
10.20280.09970.20932.3912-2.24053.5762-0.0344-0.0212-0.0097-0.3671-0.3365-0.38110.64220.53470.03950.55540.12340.09190.4295-0.00970.51938.325105.31983.4616
22.0178-0.45591.58131.1428-1.8383.3516-0.14880.2657-0.1753-1.3203-0.4226-0.83880.88151.2870.31832.2825-0.76030.75752.64360.47650.162347.1825148.1887-65.6451
32.00190.28-0.21533.0814-4.12816.8196-0.07090.27680.27430.10730.75510.4844-0.4196-1.4444-0.62070.6152-0.0002-0.02150.3028-0.04380.54225.2572123.8431-11.6898
45.9081-1.7325-0.01012.33991.01060.30480.32121.3304-0.7333-0.2525-0.14690.15660.41170.8161-0.22850.58590.1243-0.05760.6194-0.13740.589118.57799.7991-33.6741
55.25085.31716.5995.40146.75038.4642-0.24980.72981.0396-0.56710.1454-0.0866-0.0578-0.1384-0.28060.64610.17360.00450.62250.09990.53859.0779114.558-37.7357
64.56552.61641.65426.33612.05563.0906-0.16610.84980.0115-0.58670.13620.64490.0656-0.1642-0.04690.47710.1155-0.12310.649-0.0560.55586.346107.0266-37.0782
74.89050.26731.1873.27691.00672.72810.431-0.0341-0.38260.4754-0.19610.05970.38390.0733-0.14450.39780.1138-0.0490.3926-0.02010.411317.0112103.1579-25.2246
82.3724-1.6906-0.60271.6794-1.19685.09610.16280.5659-0.0956-0.3544-0.3756-0.2073-0.31470.37490.27690.45560.0877-0.03110.6032-0.00350.599415.9117107.4133-33.1336
95.85240.20561.54523.0189-0.10033.71550.075-0.07330.3552-0.067-0.26450.4164-0.0082-0.44620.20360.42040.00560.06350.45-0.0520.50424.8807106.9841-28.1846
104.1665-0.92713.19192.97680.73413.53851.1277-2.5927-1.35380.835-0.11340.46740.0991-0.6631-0.94880.6813-0.0082-0.04160.8640.18990.828912.9526102.4695-17.0548
111.39480.9519-1.2180.8765-0.72612.1819-0.0918-0.3112-0.2386-0.0516-0.1683-0.1440.20530.68840.06870.38410.0224-0.02460.60610.06230.516558.2758139.7556-3.4558
121.8616-1.2944-2.58790.93441.87283.6671-0.2843-0.9553-0.38440.4083-0.2093-0.0556-0.17751.03030.18852.303-0.19360.21591.77910.24450.969325.5228110.40865.3427
132.82570.7619-3.66112.5381-2.327.24240.59910.06910.5190.53810.28340.5743-0.8587-0.7421-0.53570.3923-0.14960.01760.6016-0.04730.572535.5204141.792911.5819
145.9042-1.32510.37936.14833.7152.91280.93311.46610.29440.04130.4915-0.4162-0.25961.2633-0.05720.43420.103-0.07270.7836-0.0730.71756.1988153.800520.3266
155.9883-0.9933-0.80694.7756-0.33860.1494-0.5008-0.80130.53130.2296-0.1235-0.58390.8131.00210.08570.40970.1081-0.06110.7632-0.13780.486957.0156159.260433.9322
163.7227-3.0858-1.19193.1220.83610.4489-1.2195-1.40430.37260.99560.94220.26330.48570.71650.26050.78980.1999-0.12391.136-0.16820.554147.1777163.466343.7154
174.53352.86172.80532.3222.09522.105-0.7289-1.1727-0.76411.2415-0.12160.95740.28340.53740.05750.5570.01930.09930.76610.07120.464435.779160.095937.8894
181.95971.02351.37743.84365.45947.94290.0022-0.3679-0.43570.6878-0.00310.04220.18020.0789-0.19590.3960.0460.02510.4929-0.03330.482339.6838159.381335.4102
192.5873-0.47220.22133.20790.62082.8015-0.2417-0.31050.57540.33380.2450.1119-0.22220.09470.00380.37570.053-0.03030.5971-0.09290.446647.5358166.578430.7949
202.8113-0.0319-0.07665.763.86884.5066-0.3546-0.04410.2904-0.16060.8119-0.55930.06470.6726-0.48010.29820.02710.02030.4751-0.04240.440948.8934157.167724.8461
213.5669-1.18780.56952.7536-0.46894.7231-0.2849-0.8409-0.38930.37720.4278-0.57150.38710.2747-0.05640.44880.137-0.01720.6397-0.00450.626845.3165157.829133.1795
223.3768-1.4247-0.61514.71960.94173.0926-0.0854-0.15680.4418-0.09060.23160.3281-0.2527-0.2776-0.06740.38790.0225-0.07880.47660.00490.536640.1814167.620128.3047
232.0718-0.391-3.2152.11190.33497.05620.55331.29451.3671-1.69090.08070.2038-0.96820.7757-0.39170.85590.0403-0.00460.85690.17440.91448.4088163.410116.8835
241.7008-0.69211.44030.4918-0.83382.845-0.3291-0.09460.2330.16090.0598-0.1059-0.6667-0.15710.0290.5660.0882-0.01590.4498-0.06930.547645.681992.6867-3.2289
251.7458-1.23060.76812.7134-2.71932.824-0.1536-0.35770.53820.57390.1918-0.1897-1.0845-0.69910.16081.6281-0.2338-0.25232.1416-0.18930.577987.561579.566365.2872
264.2402-0.644.09521.4415-1.41173.65460.613-0.5314-0.9763-0.06650.40330.08120.838-0.6339-0.59110.42240.13850.05140.51550.04750.561255.327972.113711.6499
275.23871.6349-0.28394.0575-0.10171.14940.40350.12490.47670.1594-0.39690.6535-1.4188-0.83050.04320.70720.1690.13630.38240.03440.601331.600982.921228.3376
282.7597-0.34430.16285.825-0.93820.40590.4732-0.2934-0.28651.9784-0.3853-0.0201-0.40.1501-0.01580.97350.01540.04630.53540.06130.452234.110567.971541.4072
295.27763.5351-6.76943.8823-3.5449.43520.1775-0.2544-0.16560.3887-0.35-0.5053-0.2912-0.2512-0.0480.5570.01460.02830.36210.08840.604237.876566.943735.587
305.66370.8712-2.08353.6931-0.67943.74540.21230.30970.14540.4464-0.06760.5545-0.2558-0.2579-0.08060.5290.05270.04890.34150.00990.426631.232572.960728.1851
311.2215-2.02851.23933.4357-1.75254.4151-0.176-0.1730.57720.9579-0.04670.4433-0.4631-0.46020.32580.6138-0.04790.15220.3591-0.08480.626128.69471.843335.8241
320.0229-0.02950.01680.03480.06390.1551-0.29570.16790.73050.55370.5671-1.3697-0.1261.262-0.43870.5837-0.0297-0.1710.7018-0.0921.103447.305573.284729.8552
334.90981.7927-1.30535.5956-1.24413.5466-0.18290.4282-0.77160.40590.1160.00460.4521-0.22780.0270.4262-0.00540.03080.3963-0.09620.520930.430963.28428.4556
346.36683.4746-0.70852.7271-1.74882.35630.23611.3522-0.0384-1.57070.47280.64130.5774-0.5492-0.67630.90950.0533-0.12260.70630.00460.800330.783172.732617.3156
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 190 through 298 )
2X-RAY DIFFRACTION2chain 'A' and (resid 299 through 316 )
3X-RAY DIFFRACTION3chain 'A' and (resid 317 through 362 )
4X-RAY DIFFRACTION4chain 'B' and (resid 86 through 106 )
5X-RAY DIFFRACTION5chain 'B' and (resid 107 through 112 )
6X-RAY DIFFRACTION6chain 'B' and (resid 113 through 126 )
7X-RAY DIFFRACTION7chain 'B' and (resid 127 through 151 )
8X-RAY DIFFRACTION8chain 'B' and (resid 152 through 170 )
9X-RAY DIFFRACTION9chain 'B' and (resid 171 through 195 )
10X-RAY DIFFRACTION10chain 'B' and (resid 196 through 205 )
11X-RAY DIFFRACTION11chain 'E' and (resid 190 through 298 )
12X-RAY DIFFRACTION12chain 'E' and (resid 299 through 316 )
13X-RAY DIFFRACTION13chain 'E' and (resid 317 through 362 )
14X-RAY DIFFRACTION14chain 'F' and (resid 86 through 91 )
15X-RAY DIFFRACTION15chain 'F' and (resid 92 through 99 )
16X-RAY DIFFRACTION16chain 'F' and (resid 100 through 106 )
17X-RAY DIFFRACTION17chain 'F' and (resid 107 through 112 )
18X-RAY DIFFRACTION18chain 'F' and (resid 113 through 120 )
19X-RAY DIFFRACTION19chain 'F' and (resid 121 through 137 )
20X-RAY DIFFRACTION20chain 'F' and (resid 138 through 151 )
21X-RAY DIFFRACTION21chain 'F' and (resid 152 through 170 )
22X-RAY DIFFRACTION22chain 'F' and (resid 171 through 195 )
23X-RAY DIFFRACTION23chain 'F' and (resid 196 through 205 )
24X-RAY DIFFRACTION24chain 'I' and (resid 190 through 298 )
25X-RAY DIFFRACTION25chain 'I' and (resid 299 through 316 )
26X-RAY DIFFRACTION26chain 'I' and (resid 317 through 362 )
27X-RAY DIFFRACTION27chain 'J' and (resid 86 through 99 )
28X-RAY DIFFRACTION28chain 'J' and (resid 100 through 112 )
29X-RAY DIFFRACTION29chain 'J' and (resid 113 through 120 )
30X-RAY DIFFRACTION30chain 'J' and (resid 121 through 151 )
31X-RAY DIFFRACTION31chain 'J' and (resid 152 through 162 )
32X-RAY DIFFRACTION32chain 'J' and (resid 163 through 170 )
33X-RAY DIFFRACTION33chain 'J' and (resid 171 through 195 )
34X-RAY DIFFRACTION34chain 'J' and (resid 196 through 204 )

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