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- PDB-6ymj: Crystal structure of the SAM-SAH riboswitch with adenosine. -

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Basic information

Entry
Database: PDB / ID: 6ymj
TitleCrystal structure of the SAM-SAH riboswitch with adenosine.
Components
  • Chains: A,C,F,I,M,O
  • Chains: B,D,G,J,N,P
KeywordsRNA / Pseudoknot / SAM / Riboswitch
Function / homologyADENOSINE / 5-BROMOCYTIDINE 5'-(DIHYDROGEN PHOSPHATE) / RNA / RNA (> 10)
Function and homology information
Biological speciesRoseobacter sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsHuang, L. / Lilley, D.M.J.
Funding support United Kingdom, China, 2items
OrganizationGrant numberCountry
Cancer Research UKA18604 United Kingdom
Ministry of Education (MoE, China) China
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Crystal structure and ligand-induced folding of the SAM/SAH riboswitch.
Authors: Huang, L. / Liao, T.W. / Wang, J. / Ha, T. / Lilley, D.M.J.
History
DepositionApr 8, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Apr 13, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / database_2 / entity / ndb_struct_conf_na / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _atom_site_anisotrop.id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_site.details / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id / _struct_site_gen.label_seq_id
Revision 2.1Mar 8, 2023Group: Structure summary / Category: struct / Item: _struct.title
Revision 2.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chains: A,C,F,I,M,O
B: Chains: B,D,G,J,N,P
C: Chains: A,C,F,I,M,O
D: Chains: B,D,G,J,N,P
F: Chains: A,C,F,I,M,O
G: Chains: B,D,G,J,N,P
I: Chains: A,C,F,I,M,O
J: Chains: B,D,G,J,N,P
M: Chains: A,C,F,I,M,O
N: Chains: B,D,G,J,N,P
O: Chains: A,C,F,I,M,O
P: Chains: B,D,G,J,N,P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,01727
Polymers67,71412
Non-polymers3,30315
Water66737
1
A: Chains: A,C,F,I,M,O
B: Chains: B,D,G,J,N,P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8435
Polymers11,2862
Non-polymers5573
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Chains: A,C,F,I,M,O
D: Chains: B,D,G,J,N,P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9795
Polymers11,2862
Non-polymers6943
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
F: Chains: A,C,F,I,M,O
G: Chains: B,D,G,J,N,P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8204
Polymers11,2862
Non-polymers5342
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
I: Chains: A,C,F,I,M,O
J: Chains: B,D,G,J,N,P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5533
Polymers11,2862
Non-polymers2671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
M: Chains: A,C,F,I,M,O
N: Chains: B,D,G,J,N,P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8666
Polymers11,2862
Non-polymers5804
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
O: Chains: A,C,F,I,M,O
P: Chains: B,D,G,J,N,P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9554
Polymers11,2862
Non-polymers6692
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.599, 147.570, 75.013
Angle α, β, γ (deg.)90.000, 91.358, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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RNA chain , 2 types, 12 molecules ACFIMOBDGJNP

#1: RNA chain
Chains: A,C,F,I,M,O


Mass: 8389.874 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) Roseobacter sp. (bacteria)
#2: RNA chain
Chains: B,D,G,J,N,P


Mass: 2895.791 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) Roseobacter sp. (bacteria)

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Non-polymers , 5 types, 52 molecules

#3: Chemical
ChemComp-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C10H13N5O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CBV / 5-BROMOCYTIDINE 5'-(DIHYDROGEN PHOSPHATE)


Type: RNA linking / Mass: 402.093 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13BrN3O8P
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.66 Å3/Da / Density % sol: 66.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.01 M Magnesium Sulfate, 0.05 M Sodium Cacodylate pH 6.0, 1.8 M Lithium Sulfate monohydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9119 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9119 Å / Relative weight: 1
ReflectionResolution: 2.04→74.99 Å / Num. obs: 90426 / % possible obs: 99.8 % / Redundancy: 3.3 % / Biso Wilson estimate: 63.49 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.035 / Net I/σ(I): 11
Reflection shellResolution: 2.04→2.08 Å / Redundancy: 3.4 % / Rmerge(I) obs: 1.3 / Mean I/σ(I) obs: 0.2 / Num. unique obs: 2973 / CC1/2: 0.33 / Rpim(I) all: 0.86 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YL5
Resolution: 2.04→37.34 Å / SU ML: 0.3513 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.9922
RfactorNum. reflection% reflection
Rfree0.2325 4345 4.81 %
Rwork0.1978 --
obs0.1993 90426 76.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 72.16 Å2
Refinement stepCycle: LAST / Resolution: 2.04→37.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 4326 301 37 4664
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00155145
X-RAY DIFFRACTIONf_angle_d0.47957959
X-RAY DIFFRACTIONf_chiral_restr0.01811068
X-RAY DIFFRACTIONf_plane_restr0.0024219
X-RAY DIFFRACTIONf_dihedral_angle_d13.67642436
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.04-2.060.611460.351685X-RAY DIFFRACTION2.3
2.06-2.090.619910.4552120X-RAY DIFFRACTION3.1
2.09-2.110.32860.3799157X-RAY DIFFRACTION4.29
2.11-2.140.397680.409234X-RAY DIFFRACTION6.1
2.14-2.170.3573310.3834611X-RAY DIFFRACTION16.53
2.17-2.20.3944660.38781136X-RAY DIFFRACTION30.19
2.2-2.230.38461360.36042143X-RAY DIFFRACTION58.32
2.23-2.260.36031780.36453060X-RAY DIFFRACTION81.62
2.26-2.30.38861890.37883267X-RAY DIFFRACTION89
2.3-2.340.39311550.35083464X-RAY DIFFRACTION91.14
2.34-2.380.35831410.35293481X-RAY DIFFRACTION91.6
2.38-2.420.35461330.33233475X-RAY DIFFRACTION91.78
2.42-2.470.37651770.33933475X-RAY DIFFRACTION93.02
2.47-2.520.32962590.3223604X-RAY DIFFRACTION96.91
2.52-2.570.30681990.30273599X-RAY DIFFRACTION97.41
2.57-2.630.32441940.29533667X-RAY DIFFRACTION97.65
2.63-2.70.32272100.29973605X-RAY DIFFRACTION97.35
2.7-2.770.32792590.30713594X-RAY DIFFRACTION96.88
2.77-2.850.31511930.31953587X-RAY DIFFRACTION96.55
2.85-2.940.27061680.28763596X-RAY DIFFRACTION96.19
2.94-3.050.26691210.2483620X-RAY DIFFRACTION94.42
3.05-3.170.30342200.23123418X-RAY DIFFRACTION92.45
3.17-3.310.23591570.20833648X-RAY DIFFRACTION96.06
3.31-3.490.2171790.1893632X-RAY DIFFRACTION98.22
3.49-3.710.16611910.1743671X-RAY DIFFRACTION97.48
3.71-3.990.20141470.15043675X-RAY DIFFRACTION96.81
3.99-4.390.18521840.14023608X-RAY DIFFRACTION95.88
4.39-5.030.15361910.1433497X-RAY DIFFRACTION93.18
5.03-6.330.20831030.13533758X-RAY DIFFRACTION98.34
6.33-37.340.18091430.15173594X-RAY DIFFRACTION94.46
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)
10.5369134196810.821689836692-0.1457205375450.555318928716-0.2315340218521.622720991710.0837081998278-0.2214511431170.398222781324-0.401226910887-0.1225841070420.276882168261-0.0775381893504-0.0241558089666-0.0003069780907450.6057856729520.00981789412904-0.0405644018090.5915998748090.04371299785530.53651761338130.871663791713.225260163122.6521346535
20.449831232359-0.01914153113390.0785081470720.05050119127130.01310148489710.1059648315940.17752202446-0.0471298096489-0.6139450379260.063255673109-0.503978915553-0.310004685775-0.06261190010380.1685340837280.0003713475873370.577797488894-0.06845082591890.09944277903460.6865047484030.03364119001620.6332934367944.514200398612.086570928930.3131764556
30.1810203551750.1703851204810.05164959825011.22164504601-0.7381704408060.24007440562-0.0652015390689-0.1913547830140.18720209062-0.417459485370.02898512534760.4553489586260.0175085922517-0.124127385999-0.000759051455730.580430059287-0.00864716234732-0.01299368039360.7188668036480.06280524509520.66019957711525.57180148811.979471842321.1932283011
40.3424049536780.3526723837350.5977145360080.01879720418130.1819741151720.1111718535140.06918736461920.4119548169480.5955598528090.254436252625-0.2320923386980.188731082211-0.6763908662370.544190340915-0.0005459832093950.635792354789-0.003772453279980.09055473303040.702474618050.06483392247640.7164053564745.44023615423.119260135727.6866493808
50.9705552620270.0488661937052.14682455081.7554391062-0.6730493406341.39791070684-0.537147801430.3906634825670.475980333494-0.4956847478420.147685106574-0.391428669307-0.2105373084420.272682967669-0.000718084151510.648875054643-0.1445621607090.05004961590450.967469160655-0.05677083870310.733226544675-8.73292993551.35620365129.79507526561
61.08758604075-0.7802878729170.9660013578710.619535446434-0.3254861642040.586322024578-0.5875536644930.8481109764680.44605930654-0.445551844840.247791422838-0.679111525731-0.3409326841870.07148174318210.0005797953102260.745092219617-0.239156727778-0.02284945283671.04636472359-0.004320076836030.8869247579950.4345364948556.920442514612.7550246493
70.4046659826180.490829536889-1.080977114333.04936423376-1.466146740792.28818061411-0.1788036125140.4945035506320.0528495002895-0.5366288427990.309007153361-0.6628059135420.2506152748830.436372774781-4.42492436595E-50.739494703934-0.078111866674-0.002194307356560.936767379019-0.1128383648090.538497993649-13.9897737292-10.735198881411.0814078441
81.021292847450.2015238357420.1668823575520.268457731771-0.3430303162021.70002881808-0.1376701011060.297222039559-0.4607900859090.04477415393390.1805578665880.1138783154160.1261749950160.0694496945501-0.0003396424098720.5499372529180.01285784489150.007041732912580.587943042969-0.08434647723850.495194130295-5.6378726587257.4453006622.6171521657
90.524394883547-0.716028694336-0.1695231785410.8281852156660.2857089891410.126461254538-0.326935440045-0.199192262290.431475463526-0.00781816354171-0.0299075223257-0.591510461761-0.0358635502979-0.3072241703430.0001981670172240.5513472313230.0981099296147-0.01143982787860.6021798497270.07174635283320.467083508947-11.659338952470.057320818529.9523447672
101.211123745051.166610828020.8704496576271.170754795190.8903966188240.752732789282-0.01448252439910.321709744264-0.617837561435-0.08537963313620.214366267118-0.04775305189970.1245517171740.137786801079-0.0004164316036980.5986319425050.110124862482-0.03938752645770.602879474514-0.02959553810910.466278679067-1.9056918657653.5275024421.3601734899
110.876892822463-0.391114021638-0.9864710668640.487771940043-0.05104374355980.788251881579-0.00361202227529-0.219648600618-0.429481868363-0.116833097019-0.06758799528460.484988773268-0.222531533776-0.655307715972-0.000678174945310.6075289267760.0575196663718-0.06404761970950.6241738376450.06897441903510.562348867485-21.625806737665.385286717727.2014816882
122.072063684840.4720813628330.9674741879280.2393933860661.597121713861.75198658642-0.3753088532630.630851796560.4473262744080.236977221383-0.3186565582810.49978040213-0.0118543039966-0.165109761567-0.0006844535564090.7557463270850.1789592610430.07467084645740.7093907843940.2160872284061.134927742724.999605436329.7993694738.50029665863
131.04956142834-0.99520058671-0.3763262561240.9285017333810.5185116378550.231008524073-0.121640107586-0.9218268102561.330428690070.409104385366-0.6588194858461.49054031812-0.382855828878-0.690762017614-0.1718983082240.6837916190740.26665798259-0.08245807340150.57612617126-0.0955611973811.8633362397724.145994482336.198113498510.9500895723
140.040134536266-0.0468376655313-0.1041796807520.2052800790440.2830013420990.2260582937380.4378365073680.3041957959261.012798352180.11995217755-0.4275796371080.8627153696490.5018636009390.2805336122290.0007946207392010.8307163528430.149441668110.06278813688531.14675559505-0.1895845108961.350775380276.64224157134.41065632911.0835567143
152.964579726982.24253179042.042760551251.440010137671.113020343952.41335110295-0.09757764045220.7497180765821.05235268577-0.1387588470750.1745303008650.831574779927-0.1888260781510.605491400111-0.0006465134009270.7118806869710.06829115624-0.003349557844350.7931507931920.2390757127840.94101901220638.038485146831.49674207419.82058637083
160.145451512912-0.123328919434-0.165193691860.337702398076-0.1662648710240.412254458161-0.262477426622-0.168182171106-0.170394194563-0.814663222051-0.341327655125-0.9145788534560.2349867188080.27122493032-0.001074759304840.766620972235-0.05444998974250.1507812153450.6392418187050.1166235910560.719291659989-22.686847792314.942743145825.4106405712
170.4152080312040.2545214766870.02492252621520.224962872679-0.1531025907910.5987357663560.4006372680530.5315281490980.07224586516180.584483450337-0.4182473341830.08347138656710.367339112938-0.00279101429883-0.0005560417310340.64227067548-0.02852576282330.06807543049920.677739424723-0.04551397268630.452062473861-30.9458980643-5.7000248087120.9643925733
180.1876036046470.284586311329-0.007368722634010.9211181006-0.473767559980.2746802159140.06787868240010.2172203782320.2345851264440.0537489584159-0.1988292514350.4630883426540.0306318522567-0.07001410944325.83647987647E-50.604656195248-0.06563567146730.003644462990180.567097568493-0.1131473904640.512980668158-35.1332683275-7.1639543900830.5209764306
192.03724010153-0.994865569748-0.5770542630430.8768812486050.6803919821510.3205925770620.3081452337170.3053606110280.616564431404-0.230312848912-0.382164292774-0.185644965373-0.2586995134320.183098488072-0.001063619654410.742946875514-0.1174718785970.08560402963820.608945407395-0.02128527197370.568564717882-25.36090988389.5666032389721.8549415518
200.3050473171350.6850771439550.371656369292-0.03243125458410.0521688044140.583317414464-0.3004707571720.0425802755338-0.21843081018-0.2818598768120.0775144090130.002220899993690.4681962780930.200247582634-0.0003280520618290.657051521594-0.05472462346450.01663534115450.638013083063-0.09051540767670.465784069075-25.8299066739-13.360426654728.1383894135
210.186094086389-0.03299051102640.280316018503-0.0543163383183-0.1298741548180.257749907860.325504864071-0.3176525810870.3613180797270.215167364413-0.579139593170.4490105751980.03433915590960.686323451626-0.0004372292732871.00804928799-0.03250084224810.2291621567560.7171790338610.1902201352581.28022979275-13.383523704631.88162065916.693071575
220.566485863149-2.35359499441-0.9169773198041.78069099822-0.7573712042411.39608765451-0.06525363200030.0258504201974-1.01273385967-0.583360508985-0.4032691946310.8160093387460.3731073663570.04118545754860.0002601125216150.893874443385-0.0225380194911-0.1182853284980.552082753654-0.032013171851.18893931381-18.032494808641.42564553537.9022083016
232.37484422665-2.00906006727-1.466265344921.349519458341.349064486052.855093803410.1725964937680.380127684862-1.28308262163-0.338171731981-0.3882479099690.626555554666-0.309548394462-0.636363057552-0.001132733930040.725248357267-0.00707652400675-0.1950909325040.718665838994-0.07538385718140.836117199933-24.919893239554.50076440279.37038120198
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 17 )
2X-RAY DIFFRACTION2chain 'A' and (resid 18 through 22 )
3X-RAY DIFFRACTION3chain 'A' and (resid 23 through 32 )
4X-RAY DIFFRACTION4chain 'B' and (resid 43 through 51 )
5X-RAY DIFFRACTION5chain 'C' and (resid 7 through 22 )
6X-RAY DIFFRACTION6chain 'C' and (resid 23 through 32 )
7X-RAY DIFFRACTION7chain 'D' and (resid 43 through 51 )
8X-RAY DIFFRACTION8chain 'F' and (resid 7 through 17 )
9X-RAY DIFFRACTION9chain 'F' and (resid 18 through 22 )
10X-RAY DIFFRACTION10chain 'F' and (resid 23 through 32 )
11X-RAY DIFFRACTION11chain 'G' and (resid 43 through 51 )
12X-RAY DIFFRACTION12chain 'I' and (resid 7 through 22 )
13X-RAY DIFFRACTION13chain 'I' and (resid 23 through 27 )
14X-RAY DIFFRACTION14chain 'I' and (resid 28 through 32 )
15X-RAY DIFFRACTION15chain 'J' and (resid 43 through 51 )
16X-RAY DIFFRACTION16chain 'M' and (resid 7 through 12 )
17X-RAY DIFFRACTION17chain 'M' and (resid 13 through 17 )
18X-RAY DIFFRACTION18chain 'M' and (resid 18 through 22 )
19X-RAY DIFFRACTION19chain 'M' and (resid 23 through 32 )
20X-RAY DIFFRACTION20chain 'N' and (resid 43 through 51 )
21X-RAY DIFFRACTION21chain 'O' and (resid 7 through 12 )
22X-RAY DIFFRACTION22chain 'O' and (resid 13 through 32 )
23X-RAY DIFFRACTION23chain 'P' and (resid 43 through 51 )

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