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- PDB-4k6l: Structure of Typhoid Toxin -

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Basic information

Entry
Database: PDB / ID: 4k6l
TitleStructure of Typhoid Toxin
Components
  • (Putative pertussis-like toxin subunit) x 2
  • Cytolethal distending toxin subunit B homolog
KeywordsTOXIN / complex / bacterial toxin / sugar
Function / homology
Function and homology information


NAD+ poly-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / toxin activity / endonuclease activity / Hydrolases; Acting on ester bonds / extracellular region
Similarity search - Function
Cytolethal distending toxin B / Bordetella pertussis toxin A / Pertussis toxin, subunit 1 / Bordetella pertussis toxin B, subunit 2/3, C-terminal / Pertussis toxin, subunit 2 and 3, C-terminal domain / Heat-Labile Enterotoxin; Chain A / Heat-Labile Enterotoxin, subunit A / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #110 ...Cytolethal distending toxin B / Bordetella pertussis toxin A / Pertussis toxin, subunit 1 / Bordetella pertussis toxin B, subunit 2/3, C-terminal / Pertussis toxin, subunit 2 and 3, C-terminal domain / Heat-Labile Enterotoxin; Chain A / Heat-Labile Enterotoxin, subunit A / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #110 / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Enterotoxin / Endonuclease/exonuclease/phosphatase superfamily / 4-Layer Sandwich / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Prokaryotic membrane lipoprotein lipid attachment site profile. / Alpha-Beta Complex / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Pertussis-like toxin subunit / Pertussis toxin-like subunit ArtA / Cytolethal distending toxin subunit B homolog
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhi (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.393 Å
AuthorsGao, X. / Song, J. / Galan, J.
CitationJournal: Nature / Year: 2013
Title: Structure and function of the Salmonella Typhi chimaeric A(2)B(5) typhoid toxin.
Authors: Song, J. / Gao, X. / Galan, J.E.
History
DepositionApr 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Database references
Revision 1.2Jul 31, 2013Group: Database references
Revision 1.3Oct 29, 2014Group: Structure summary
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative pertussis-like toxin subunit
B: Putative pertussis-like toxin subunit
C: Putative pertussis-like toxin subunit
D: Putative pertussis-like toxin subunit
E: Putative pertussis-like toxin subunit
F: Cytolethal distending toxin subunit B homolog
G: Putative pertussis-like toxin subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,81915
Polymers116,0827
Non-polymers7378
Water6,882382
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18360 Å2
ΔGint-67 kcal/mol
Surface area37440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.386, 261.076, 109.896
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-328-

HOH

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Components

#1: Protein
Putative pertussis-like toxin subunit


Mass: 12563.042 Da / Num. of mol.: 5 / Fragment: unp residues 24-137
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhi (bacteria)
Gene: STY1891, t1107 / Plasmid: PET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8Z6A3
#2: Protein Cytolethal distending toxin subunit B homolog / CDT B / Deoxyribonuclease CdtB


Mass: 28149.777 Da / Num. of mol.: 1 / Fragment: unp residues 23-269
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhi (bacteria)
Gene: cdtB, STY1886, t1111 / Plasmid: PET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q8Z6A7, Hydrolases; Acting on ester bonds
#3: Protein Putative pertussis-like toxin subunit


Mass: 25117.145 Da / Num. of mol.: 1 / Fragment: unp residues 19-242
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhi (bacteria)
Gene: STY1890, t1108 / Plasmid: PET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q8Z6A4, Transferases; Glycosyltransferases; Pentosyltransferases
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.42 Å3/Da / Density % sol: 49.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 1.6 M sodium formate and 0.1 M sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jan 9, 2013 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→32 Å / Num. all: 43611 / Num. obs: 43127 / % possible obs: 0.989 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.5 % / Biso Wilson estimate: 41.49 Å2 / Rmerge(I) obs: 0.097
Reflection shellResolution: 2.4→2.49 Å / % possible all: 95.9

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASESphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID, 1SR4, 1PRT, 3DWP

1sr4

1prt

3dwp


Resolution: 2.393→31.908 Å / SU ML: 0.27 / σ(F): 1.33 / Phase error: 29.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2532 2189 5.08 %
Rwork0.2075 --
obs0.2098 43127 96.06 %
all-43611 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.393→31.908 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8102 0 48 382 8532
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048357
X-RAY DIFFRACTIONf_angle_d0.83911358
X-RAY DIFFRACTIONf_dihedral_angle_d11.3182939
X-RAY DIFFRACTIONf_chiral_restr0.0541263
X-RAY DIFFRACTIONf_plane_restr0.0041454
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3935-2.44550.34421290.29922375X-RAY DIFFRACTION91
2.4455-2.50230.33731480.29692518X-RAY DIFFRACTION96
2.5023-2.56490.31541270.28712501X-RAY DIFFRACTION96
2.5649-2.63420.38081280.27912531X-RAY DIFFRACTION96
2.6342-2.71170.3221450.2762532X-RAY DIFFRACTION96
2.7117-2.79920.30981240.282555X-RAY DIFFRACTION96
2.7992-2.89910.29861340.27372523X-RAY DIFFRACTION95
2.8991-3.01510.34081190.25692541X-RAY DIFFRACTION96
3.0151-3.15220.31961310.26392530X-RAY DIFFRACTION96
3.1522-3.31830.25731480.24192557X-RAY DIFFRACTION97
3.3183-3.52590.27841510.22162543X-RAY DIFFRACTION97
3.5259-3.79780.25181240.19682597X-RAY DIFFRACTION96
3.7978-4.17920.24511350.18152521X-RAY DIFFRACTION94
4.1792-4.78220.17951290.14392628X-RAY DIFFRACTION97
4.7822-6.01850.1981510.1592687X-RAY DIFFRACTION99
6.0185-31.91070.19321660.16742799X-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)
10.5741.78380.6667.6857-1.32586.1517-0.20610.04780.39890.12510.25360.7224-0.8821-0.4154-0.06340.69390.0590.11570.22560.09830.95358.624370.878710.8082
21.82781.33260.91713.26860.51292.3640.08040.18630.7779-0.91350.15290.1691-0.4003-0.2324-0.23410.61870.11480.12510.38210.22870.74558.099661.167-4.0353
33.22981.79680.36173.3778-0.93361.3836-0.13310.25070.39520.18820.17240.1725-0.4092-0.0888-0.08550.9046-0.07080.20070.3260.25630.837614.094262.7245-5.8617
40.0113-0.0021-0.00390.0044-0.00320.0044-0.15230.30980.3578-0.33250.03990.9636-0.5576-0.76060.06830.81420.3995-0.17610.85720.03240.8026-4.601561.5887-7.1833
51.20231.71960.69694.68620.74581.86660.24860.3880.7825-0.39930.2631-0.5077-0.58780.1523-0.36190.575-0.05450.18390.30380.05830.716315.226159.8960.8589
63.54620.63911.25220.65351.48993.41-0.11950.13180.51180.13990.08150.2258-0.04660.1953-0.00640.49810.07720.01120.39880.18760.7764.272661.22882.8647
70.5413-0.1660.47081.5890.41430.61210.10930.17260.2098-0.35230.0208-0.2905-0.32030.14740.11821.361-0.01740.39150.48670.36451.149813.781672.1731-8.1056
83.83111.80380.37180.8918-0.14182.46290.5176-0.07380.495-0.2408-0.40580.1683-0.5088-0.2466-0.07510.52530.02110.07010.24540.02120.64652.038359.82317.7589
92.32720.5717-0.27681.2130.23751.32130.1262-0.23150.5405-0.0063-0.0291-0.0306-0.33080.1461-0.12120.3093-0.03940.00630.2433-0.04060.370310.462651.779919.5618
103.97860.94060.44833.1995-0.42043.65650.1704-0.19510.53190.0741-0.1199-0.4046-0.64060.3177-0.08650.3208-0.03560.00940.2455-0.03950.40997.776552.963319.8759
111.8596-0.82560.36343.5474-0.28532.62490.0928-0.11030.4640.07220.0059-0.1045-0.33120.3881-0.11180.1983-0.06510.03890.2815-0.0260.374511.829749.510519.3727
120.22190.41670.41282.8363-0.441.96560.30550.26020.54170.0056-0.1447-0.1391-0.61120.0718-0.04031.27060.17920.35490.72690.4840.973721.184662.7131-19.5056
130.4896-0.6962-0.95772.4374-0.19423.53090.43020.19910.5545-0.24870.1484-0.0562-0.7073-0.0522-0.47370.487-0.02350.18760.49620.21720.645828.023746.4751-14.565
143.8056-0.4672-1.04744.576-0.94722.09260.73580.86720.6985-0.406-0.1811-0.3106-0.8386-0.2155-0.53030.78340.02580.28860.74930.09510.582326.174950.6984-18.8555
152.4323-0.6309-1.04892.65820.84951.830.4564-0.11330.6658-0.1324-0.06710.1885-0.67040.0902-0.42070.6397-0.00930.19520.49410.22020.6522.923252.0638-7.9617
160.8909-1.73150.57863.5622-0.42182.88150.45630.06580.4553-0.58-0.0123-0.1208-0.7499-0.0624-0.3550.84850.15370.24130.75670.31670.614818.139554.6561-17.4828
171.50420.03330.40440.0884-0.08690.2101-0.0020.03120.07210.02250.0210.0309-0.10810.07490.06491.067-0.26290.58090.88660.17811.171436.136555.0979-20.6069
182.36290.37750.26530.794-0.28110.37540.19560.67840.553-0.56450.0704-0.1959-0.39220.0485-0.18040.90990.04960.37090.62710.24960.764729.962551.1475-19.018
190.22220.1597-0.06380.1151-0.04270.0712-0.30650.19550.0273-0.6692-0.0313-0.0298-0.4306-0.05290.29471.11510.4150.00610.8550.28630.8429.472459.2786-17.8062
201.30231.57880.35192.22921.08641.8728-0.132-0.2569-0.1640.09930.1258-0.22110.16690.52230.03570.21630.0265-0.05680.47650.02590.274727.811730.759516.5482
212.3148-1.5907-0.00045.63192.39982.8399-0.0912-0.51830.05840.0602-0.16460.0319-0.0240.05070.23510.2238-0.03990.0230.38550.03980.279122.503837.535620.0009
222.2686-0.74030.73951.67341.72372.9330.2224-0.2549-0.11590.5872-0.1017-0.24680.24810.295-0.12460.281-0.02580.00550.49010.04310.240224.199631.881920.0048
232.309-0.64121.4392.20121.35692.4250.2739-0.19360.3573-0.1513-0.0589-0.393-0.23570.4198-0.20020.2438-0.08570.05040.40940.00970.257125.596238.082910.6162
246.4811-1.46480.0724.0005-1.36874.5555-0.1558-0.2606-0.30410.04510.0710.05410.38640.31020.09360.280600.00170.29350.03080.339226.576127.392112.5238
251.0709-0.20190.59850.6638-0.42530.73260.0624-0.7573-0.29080.31950.2267-0.25610.18520.2746-0.25840.2332-0.0082-0.06160.66350.05110.366126.860634.530524.7506
262.59893.6241-0.38625.3234-1.5884.5803-0.21860.4016-1.3075-0.1199-0.11460.05351.47750.21980.27580.51730.07150.00310.3491-0.1020.568129.399421.15555.5291
272.1265-0.43860.18221.70850.32293.8946-0.0099-0.01950.2847-0.20550.0228-0.1785-0.07230.77120.01370.1999-0.01530.03810.3624-0.01690.362835.278933.5805-4.6624
287.041-3.6611-2.10275.0386-2.93815.81210.2282-0.3174-0.0252-0.37190.06630.27710.06530.5671-0.21660.19210.00080.04240.35560.03060.306635.718230.6933-4.2816
293.4172-0.38980.54551.577-0.65224.29820.19610.0681-0.2758-0.05510.0895-0.2771-0.27740.4354-0.27380.2205-0.06850.06980.4169-0.01220.447134.985435.1471-3.7165
303.39313.1408-2.50567.76260.85193.92610.03951.26830.2541-1.51950.3680.19020.3507-0.5182-0.37170.5501-0.0875-0.00710.81510.17610.419528.811436.1465-20.5144
311.7989-0.908-1.61082.01770.05393.3912-0.17840.1086-0.4112-0.62470.056-0.3370.360.09970.09220.4355-0.06620.06770.3988-0.10170.4229-12.48114.3566-19.0291
322.6426-2.169-1.50963.9471-0.42376.1087-0.14840.014-0.3753-0.376-0.00070.01810.60670.19590.1590.51920.02160.15340.321-0.14240.4738-9.6822-0.7177-16.7257
332.21990.1240.29333.24760.22371.9773-0.22540.3302-0.0906-0.50870.18930.35440.0655-0.14770.04020.3371-0.0871-0.02210.4013-0.05470.2989-25.446312.2242-16.3682
341.64270.41740.04161.57850.99691.73270.04560.0821-0.0610.0469-0.0703-0.15430.0358-0.23080.03070.206-0.0137-0.04840.30650.05760.1998-6.207230.24973.033
353.0171.41560.97024.68130.12011.8268-0.06660.34240.0087-0.32540.0801-0.2577-0.1405-0.0095-0.00780.23660.00870.00710.34420.01930.1636-3.882931.2644-3.7658
369.7717-2.6622-4.93789.3594-2.60174.5379-0.2576-0.09980.06190.5661-0.2437-1.3005-0.15911.24780.480.29190.0105-0.02030.45230.20530.424814.848442.1421-0.1445
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 24 through 31 )
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 47 )
3X-RAY DIFFRACTION3chain 'A' and (resid 48 through 59 )
4X-RAY DIFFRACTION4chain 'A' and (resid 60 through 66 )
5X-RAY DIFFRACTION5chain 'A' and (resid 67 through 95 )
6X-RAY DIFFRACTION6chain 'A' and (resid 96 through 104 )
7X-RAY DIFFRACTION7chain 'A' and (resid 105 through 120 )
8X-RAY DIFFRACTION8chain 'A' and (resid 121 through 137 )
9X-RAY DIFFRACTION9chain 'B' and (resid 24 through 59 )
10X-RAY DIFFRACTION10chain 'B' and (resid 60 through 76 )
11X-RAY DIFFRACTION11chain 'B' and (resid 77 through 137 )
12X-RAY DIFFRACTION12chain 'C' and (resid 24 through 36 )
13X-RAY DIFFRACTION13chain 'C' and (resid 37 through 59 )
14X-RAY DIFFRACTION14chain 'C' and (resid 60 through 76 )
15X-RAY DIFFRACTION15chain 'C' and (resid 77 through 95 )
16X-RAY DIFFRACTION16chain 'C' and (resid 96 through 104 )
17X-RAY DIFFRACTION17chain 'C' and (resid 105 through 110 )
18X-RAY DIFFRACTION18chain 'C' and (resid 111 through 127 )
19X-RAY DIFFRACTION19chain 'C' and (resid 128 through 137 )
20X-RAY DIFFRACTION20chain 'D' and (resid 24 through 47 )
21X-RAY DIFFRACTION21chain 'D' and (resid 48 through 59 )
22X-RAY DIFFRACTION22chain 'D' and (resid 60 through 76 )
23X-RAY DIFFRACTION23chain 'D' and (resid 77 through 95 )
24X-RAY DIFFRACTION24chain 'D' and (resid 96 through 104 )
25X-RAY DIFFRACTION25chain 'D' and (resid 105 through 127 )
26X-RAY DIFFRACTION26chain 'D' and (resid 128 through 137 )
27X-RAY DIFFRACTION27chain 'E' and (resid 24 through 59 )
28X-RAY DIFFRACTION28chain 'E' and (resid 60 through 76 )
29X-RAY DIFFRACTION29chain 'E' and (resid 77 through 127 )
30X-RAY DIFFRACTION30chain 'E' and (resid 128 through 137 )
31X-RAY DIFFRACTION31chain 'F' and (resid 23 through 90 )
32X-RAY DIFFRACTION32chain 'F' and (resid 91 through 121 )
33X-RAY DIFFRACTION33chain 'F' and (resid 122 through 269 )
34X-RAY DIFFRACTION34chain 'G' and (resid 19 through 172 )
35X-RAY DIFFRACTION35chain 'G' and (resid 173 through 231 )
36X-RAY DIFFRACTION36chain 'G' and (resid 232 through 242 )

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Yorodumi

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  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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