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- PDB-4z9c: EcPltAB Oxidized -

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Basic information

Entry
Database: PDB / ID: 4z9c
TitleEcPltAB Oxidized
Components
  • Pertussis toxin-like subunit ArtA
  • Subtilase cytotoxin subunit B-like protein
KeywordsTRANSFERASE / Redox switch / Pertussis toxin / Typhoid toxin / ADP-ribosyltransferase / Escherichia coli / AB5
Function / homology
Function and homology information


NAD+ ADP-ribosyltransferase activity / ribosome / structural constituent of ribosome / translation / nucleotide binding / extracellular region
Similarity search - Function
Bordetella pertussis toxin A / Pertussis toxin, subunit 1 / Heat-Labile Enterotoxin; Chain A / Heat-Labile Enterotoxin, subunit A / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #110 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Ribosomal protein S9, conserved site / Ribosomal protein S9 signature. / Ribosomal protein S9 / Ribosomal protein S9/S16 ...Bordetella pertussis toxin A / Pertussis toxin, subunit 1 / Heat-Labile Enterotoxin; Chain A / Heat-Labile Enterotoxin, subunit A / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #110 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Ribosomal protein S9, conserved site / Ribosomal protein S9 signature. / Ribosomal protein S9 / Ribosomal protein S9/S16 / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / Alpha-Beta Complex / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / 40S ribosomal protein S16 / Pertussis toxin subunit 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsLittler, D.R. / Johnson, M.D. / Summers, R.J. / Schembri, M.A. / Rossjohn, J. / Beddoe, T.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Structure and function analyses of a pertussis-like toxin from pathogenic Escherichia coli reveal a distinct mechanism of inhibition of trimeric G proteins.
Authors: Littler, D.R. / Ang, S.Y. / Moriel, D.G. / Kocan, M. / Kleifeld, O. / Johnson, M.D. / Tran, M.T. / Paton, A.W. / Paton, J.C. / Summers, R. / Schrembri, M. / Rossjohn, J. / Beddoe, T.T.
History
DepositionApr 10, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / diffrn_source / pdbx_struct_oper_list
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.pdbx_database_id_PubMed / _citation.title / _citation.year / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 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: Pertussis toxin-like subunit ArtA
B: Subtilase cytotoxin subunit B-like protein
C: Subtilase cytotoxin subunit B-like protein
D: Subtilase cytotoxin subunit B-like protein
E: Subtilase cytotoxin subunit B-like protein
F: Subtilase cytotoxin subunit B-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,0777
Polymers100,9826
Non-polymers951
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13480 Å2
ΔGint-79 kcal/mol
Surface area31310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.900, 160.900, 62.640
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Pertussis toxin-like subunit ArtA / Pertussis-like toxin subunit A


Mass: 27565.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: PU15_14675, PU38_26245 / Details (production host): pUC57 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0B1KWV6, NAD+ ADP-ribosyltransferase
#2: Protein
Subtilase cytotoxin subunit B-like protein / Pertussis-like toxin subunit B


Mass: 14683.417 Da / Num. of mol.: 5 / Fragment: UNP residues 25-141
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: PU15_14670, PU38_26240 / Plasmid: pUC57 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0B1KTJ4
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 46.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M magnesium chloride, 0.1 M Tris-HCl, pH 8.5, 15% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.35→49.42 Å / Num. obs: 38825 / % possible obs: 99.9 % / Redundancy: 8.4 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 12.1
Reflection shellResolution: 2.35→2.48 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.356 / Mean I/σ(I) obs: 2.1 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3DWA
Resolution: 2.35→40.312 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1935 4.99 %Random selection
Rwork0.192 ---
obs0.1951 38796 99.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.35→40.312 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6380 0 5 64 6449
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116546
X-RAY DIFFRACTIONf_angle_d1.3728809
X-RAY DIFFRACTIONf_dihedral_angle_d14.0342372
X-RAY DIFFRACTIONf_chiral_restr0.067907
X-RAY DIFFRACTIONf_plane_restr0.0061141
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.40880.33111330.31822629X-RAY DIFFRACTION100
2.4088-2.47390.35351450.28262582X-RAY DIFFRACTION100
2.4739-2.54670.31811570.26362603X-RAY DIFFRACTION100
2.5467-2.62890.30371320.25272620X-RAY DIFFRACTION100
2.6289-2.72280.28741460.24722603X-RAY DIFFRACTION100
2.7228-2.83180.3241460.24212615X-RAY DIFFRACTION100
2.8318-2.96070.31251500.24432588X-RAY DIFFRACTION100
2.9607-3.11670.29681460.22022617X-RAY DIFFRACTION100
3.1167-3.31190.25061660.21142606X-RAY DIFFRACTION100
3.3119-3.56750.27821100.1842648X-RAY DIFFRACTION100
3.5675-3.92620.26011130.1742699X-RAY DIFFRACTION100
3.9262-4.49370.2021180.14842652X-RAY DIFFRACTION100
4.4937-5.65910.18351330.13892666X-RAY DIFFRACTION100
5.6591-40.31760.23711400.17812733X-RAY DIFFRACTION100
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)
13.8259-0.2653-1.93364.09410.13544.96490.6290.08441.1163-0.0343-0.0026-0.2086-1.03760.0129-0.45820.55750.01170.29780.3423-0.00680.8134-3.7222-34.0932-2.5441
24.04121.6405-3.50515.67821.57899.6128-0.15830.520.673-0.46250.07220.2982-0.414-0.52970.0810.34380.0427-0.00230.522-0.00770.5936-17.3807-45.5064-7.4719
34.66710.2259-0.13155.0080.08372.64750.8483-0.26651.53780.0583-0.2052-0.1175-1.04240.0778-0.51370.8455-0.05480.40190.4867-0.09551.0672-2.7709-28.63421.925
44.21761.2489-1.82972.5414-1.00954.39030.6077-0.09221.26370.1365-0.06710.2755-1.0644-0.3442-0.14280.73790.24550.42310.0956-0.07340.8007-6.7029-29.9983-0.2282
54.634-0.1342-2.55568.95552.00299.20210.15280.4352-0.0767-0.775-0.0024-0.2542-0.287-0.3357-0.14390.21560.0440.06730.3712-0.00190.4119-4.8394-45.8879-4.0166
68.1137-1.0832-0.2960.3295-0.61120.35340.18350.14950.6343-0.2304-0.07820.64060.10530.1538-0.15750.5925-0.09150.09440.5457-0.10050.973611.4446-38.5383-3.1586
71.5847-1.97091.75767.74552.45456.6844-0.211-0.30020.30420.11140.13570.37120.0810.11060.11830.2230.0560.03040.3504-0.01770.463-9.7884-54.9663-0.208
86.0124-3.18615.75029.873-2.58555.65480.3607-2.5972-0.03751.61721.41440.3908-0.2578-1.9038-0.54690.6541-0.08590.06621.0218-0.20390.2709-19.6666-44.992726.126
97.1796-3.3485-0.49147.61321.85950.9827-0.099-1.1856-0.03651.6151-0.3061-1.2796-0.12860.43490.47880.4199-0.0909-0.12540.63170.02720.3361-6.9354-58.882620.2394
107.7047-0.739-2.05977.0410.73566.8878-0.3018-1.043-1.1131.25590.3475-1.09751.0070.4280.07150.53140.044-0.16270.68330.10120.5764-9.5205-61.14623.0904
116.1222.8631-2.85763.38770.68233.28810.8431-0.4010.78780.9944-0.4598-0.1794-1.6052.1044-0.13580.9344-0.2509-0.04820.9672-0.19480.7713-6.828-40.013123.3789
123.4163-2.00571.24222.548-0.32338.01190.0281-0.6928-0.46511.05490.2261.08550.6683-0.5119-0.19320.54360.0145-0.04890.80640.19060.5984-16.443-63.584724.3288
135.3216-1.5998-0.03986.0795-6.62239.33360.116-0.6012-0.5196-0.9202-0.0538-0.17020.8249-0.1241-0.20650.31670.0164-0.0230.4128-0.04270.3058-14.8775-55.179912.8944
146.9216-0.8569-2.20176.2341-2.63229.26830.0153-1.27510.49110.9588-0.2940.1234-0.70680.21440.47480.3983-0.0804-0.00240.7105-0.11490.3736-16.9546-46.949122.2427
156.92171.8778-4.77033.9798-0.32583.54962.1026-6.4255-1.28394.64782.7255-1.35340.21032.497-3.81521.90040.4022-0.10062.11580.09691.6431-9.661-60.293233.4835
160.8037-1.5070.80212.8513-1.5160.8438-0.3834-1.9015-0.31362.31691.0559-0.8474-0.19940.8871-0.26131.13910.1609-0.49931.56070.04070.9328-4.4304-57.419930.5436
175.5608-0.7387-0.06835.3348-3.08677.17470.0523-0.83740.63511.32250.07080.0023-0.9123-0.8283-0.16780.4573-0.02990.03430.5251-0.12160.3586-21.1319-44.155619.5059
183.5053-0.7393-0.81541.56830.83151.81660.2122-0.4630.28660.1681-0.17090.4977-0.147-0.9541-0.17620.2632-0.04080.04760.602-0.0260.4265-33.8142-49.649410.216
194.43831.2824-1.84154.7461-4.65715.48910.2235-1.41850.15290.32310.06130.29870.2781-0.3213-0.32410.3879-0.02730.00670.76770.02020.2998-29.5694-53.471917.928
204.0671-0.42010.53136.4163-2.59384.3237-0.0877-0.51540.8051-0.04720.12020.4983-0.3388-0.97250.12610.37060.1150.07080.7516-0.0920.4364-33.4949-43.994411.0781
219.20297.6871-2.97867.0786-4.58989.4189-1.6374-0.754-1.3311-0.77220.9685-1.1934-0.2361-0.34730.63980.85570.1181-0.02010.833-0.07780.5929-31.9842-66.401916.5947
227.42685.7868-4.8778.404-5.61124.66020.0705-0.0988-0.3594-0.1501-0.2714-0.21130.2877-0.02410.26540.27740.00980.00890.4398-0.04890.2791-25.4209-54.37565.7465
236.5645.111-6.66174.2297-4.63697.09310.16170.1799-0.07680.0558-0.28260.4071-0.6251-1.2460.1090.2783-0.05340.07170.7088-0.13380.5137-36.5221-48.75144.1783
243.73712.0672-3.99671.8748-3.355.9204-0.5383-1.8611.94442.50232.40260.12450.8686-0.2726-1.37291.30.0253-0.11311.5937-0.29390.9384-37.2866-51.290223.7828
257.02320.2133-3.12317.6198-0.8272.1529-0.0303-0.08930.23590.15410.2489-0.09240.0408-0.8802-0.0830.24150.0294-0.00920.6133-0.12590.4101-36.6025-49.09644.1779
266.4533-3.30573.59693.17561.30198.21210.12390.8945-1.4379-0.6204-0.27910.26370.6639-1.13890.05150.3921-0.1647-0.05550.6736-0.17860.5789-30.2915-70.8267-16.9109
277.32632.2383-6.1783.1615-1.57064.8798-0.02940.24540.3076-0.08010.33350.25660.3028-0.5162-0.3350.2479-0.0673-0.09670.5377-0.01520.3059-35.816-60.8109-1.529
286.27231.3411-4.22553.4192-0.46346.9081-0.0290.4936-0.2031-0.3158-0.204-0.13670.0286-0.15590.39610.3492-0.04850.03040.6947-0.09310.6912-34.1915-64.6357-7.1018
294.47821.8181-0.74047.3389-0.67514.9920.076-0.1157-0.45510.19360.0323-0.18510.0325-0.3196-0.06010.15120.00970.01070.4555-0.04310.2856-25.9336-64.026-7.7585
307.0297-0.4497-4.27625.16311.39396.8237-0.17421.08170.3082-0.08760.2024-0.05220.2054-0.76540.04940.3786-0.0753-0.11380.5960.02580.4202-33.1208-66.8062-10.8881
313.67680.11870.27753.5799-1.04274.23530.17580.8199-1.4412-0.47780.0575-0.78360.51910.0285-0.1620.3777-0.0499-0.0490.3751-0.22480.8139-11.1158-75.9747-8.3343
327.0389-0.0919-3.60865.0546-1.52899.11560.26530.0960.49140.14760.47370.62470.346-0.6911-0.6820.2878-0.0535-0.14630.3642-0.05480.5712-20.5187-76.619-6.66
331.9944.9693-1.83775.8077-4.99297.85660.611.25090.5239-2.2371-0.33821.229-0.70251.6659-0.25130.7753-0.1370.16621.168-0.42891.1238-4.7819-72.4451-18.9835
349.34082.01660.29958.4476-0.44113.42520.1518-0.34-1.22820.31070.16560.09710.509-0.3809-0.26720.2968-0.0063-0.05030.3708-0.00860.5884-15.7107-73.3762-1.2061
357.37971.53470.5622.5012-0.7063.53470.03670.9571-1.28520.21110.40520.6970.76950.1038-0.43620.55270.03140.05150.4875-0.13271.3855-9.2381-79.1847-8.0072
368.65423.7175-4.89323.9226-0.09994.5568-0.2952.7637-1.1212-0.2384-1.23640.3472-0.8041-0.98641.23670.9331-0.0251-0.01291.086-0.42051.1666-20.1126-82.3933-14.4944
375.2168-2.1508-2.06274.88770.70043.2073-0.22210.3538-1.7416-0.11830.1963-2.31360.38330.68190.08260.46450.1124-0.00580.6238-0.09071.1791-0.0084-73.4198-4.6013
382.4712.00871.95282.86144.02295.460.5194-0.2628-0.93890.75350.0754-1.02321.01430.7212-0.40540.4920.106-0.22860.63230.16810.98391.2062-68.699211.5389
390.874-1.8065-0.44155.0772-0.70553.86620.5618-0.5454-0.91170.1966-0.5157-0.40550.32140.2449-0.05880.37960.0559-0.13210.50950.04340.97731.9252-71.11388.8645
405.11443.80845.5714.41356.15338.59740.6764-0.3039-0.77622.4765-0.70820.36012.1331-0.2275-0.07461.1443-0.1748-0.12140.81990.15591.02-13.3896-77.854216.266
410.3458-0.58010.29326.5176-2.35897.775-0.0132-0.2083-0.9509-0.047-0.2913-0.00140.2191-0.02180.14470.25160.0007-0.04470.36950.01080.5207-7.2365-63.23518.156
426.51390.1899-0.93514.14320.68727.3144-0.1635-0.7003-0.86940.99210.1105-1.1395-0.13040.44150.00520.273-0.0387-0.07390.57910.11230.64932.9643-63.52815.567
430.04840.08010.28110.060.17641.151-0.4772-1.1467-1.5242-0.6755-1.3724-1.0977-1.2983-0.92751.59421.05690.3984-0.31411.48640.32331.75851.6688-82.061313.694
446.738-4.3342-5.14.70274.39334.58091.43542.0523-1.5179-0.29-0.5336-0.64970.2868-0.3597-1.08770.90960.2935-0.13160.94970.02681.22384.6433-80.60067.3463
455.2226-4.73181.12987.4776-4.32139.1224-0.0732-0.9478-0.12391.21320.2604-0.8626-0.7450.4415-0.17110.3423-0.0298-0.08050.72340.05740.63761.9968-58.649517.9848
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 99 )
2X-RAY DIFFRACTION2chain 'A' and (resid 100 through 116 )
3X-RAY DIFFRACTION3chain 'A' and (resid 117 through 139 )
4X-RAY DIFFRACTION4chain 'A' and (resid 140 through 177 )
5X-RAY DIFFRACTION5chain 'A' and (resid 178 through 197 )
6X-RAY DIFFRACTION6chain 'A' and (resid 198 through 213 )
7X-RAY DIFFRACTION7chain 'A' and (resid 214 through 226 )
8X-RAY DIFFRACTION8chain 'B' and (resid 0 through 9 )
9X-RAY DIFFRACTION9chain 'B' and (resid 10 through 21 )
10X-RAY DIFFRACTION10chain 'B' and (resid 22 through 34 )
11X-RAY DIFFRACTION11chain 'B' and (resid 35 through 43 )
12X-RAY DIFFRACTION12chain 'B' and (resid 44 through 57 )
13X-RAY DIFFRACTION13chain 'B' and (resid 58 through 71 )
14X-RAY DIFFRACTION14chain 'B' and (resid 72 through 81 )
15X-RAY DIFFRACTION15chain 'B' and (resid 82 through 87 )
16X-RAY DIFFRACTION16chain 'B' and (resid 88 through 95 )
17X-RAY DIFFRACTION17chain 'B' and (resid 96 through 114 )
18X-RAY DIFFRACTION18chain 'C' and (resid 0 through 21 )
19X-RAY DIFFRACTION19chain 'C' and (resid 22 through 34 )
20X-RAY DIFFRACTION20chain 'C' and (resid 35 through 50 )
21X-RAY DIFFRACTION21chain 'C' and (resid 51 through 57 )
22X-RAY DIFFRACTION22chain 'C' and (resid 58 through 71 )
23X-RAY DIFFRACTION23chain 'C' and (resid 72 through 81 )
24X-RAY DIFFRACTION24chain 'C' and (resid 82 through 89 )
25X-RAY DIFFRACTION25chain 'C' and (resid 90 through 114 )
26X-RAY DIFFRACTION26chain 'D' and (resid 0 through 9 )
27X-RAY DIFFRACTION27chain 'D' and (resid 10 through 34 )
28X-RAY DIFFRACTION28chain 'D' and (resid 35 through 57 )
29X-RAY DIFFRACTION29chain 'D' and (resid 58 through 81 )
30X-RAY DIFFRACTION30chain 'D' and (resid 82 through 114 )
31X-RAY DIFFRACTION31chain 'E' and (resid 0 through 21 )
32X-RAY DIFFRACTION32chain 'E' and (resid 22 through 34 )
33X-RAY DIFFRACTION33chain 'E' and (resid 35 through 43 )
34X-RAY DIFFRACTION34chain 'E' and (resid 44 through 71 )
35X-RAY DIFFRACTION35chain 'E' and (resid 72 through 86 )
36X-RAY DIFFRACTION36chain 'E' and (resid 87 through 95 )
37X-RAY DIFFRACTION37chain 'E' and (resid 96 through 114 )
38X-RAY DIFFRACTION38chain 'F' and (resid 0 through 21 )
39X-RAY DIFFRACTION39chain 'F' and (resid 22 through 50 )
40X-RAY DIFFRACTION40chain 'F' and (resid 51 through 57 )
41X-RAY DIFFRACTION41chain 'F' and (resid 58 through 71 )
42X-RAY DIFFRACTION42chain 'F' and (resid 72 through 81 )
43X-RAY DIFFRACTION43chain 'F' and (resid 82 through 86 )
44X-RAY DIFFRACTION44chain 'F' and (resid 87 through 95 )
45X-RAY DIFFRACTION45chain 'F' and (resid 96 through 114 )

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