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- PDB-7zhl: Salmonella enterica Rhs1 C-terminal toxin TreTu -

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Basic information

Entry
Database: PDB / ID: 7zhl
TitleSalmonella enterica Rhs1 C-terminal toxin TreTu
ComponentsRHS repeat protein
KeywordsTOXIN / bacterial toxin / secreted toxin / T6SS / ADP-ribosyltransferase / translation inhibitor
Function / homology
Function and homology information


membrane => GO:0016020
Similarity search - Function
Domain of unknown function DUF6531 / Domain of unknown function (DUF6531) / RHS protein / RHS protein / RHS repeat / RHS Repeat / PAAR motif / PAAR motif / YD repeat / Rhs repeat-associated core / Quinoprotein amine dehydrogenase, beta chain-like
Similarity search - Domain/homology
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsJurenas, D. / Rey, M. / Chamot-Rooke, J. / Terradot, L. / Cascales, E.
Funding support France, 2items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-17-CE11-0039 France
Agence Nationale de la Recherche (ANR)ANR-20-CE11-0017 France
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: Salmonella antibacterial Rhs polymorphic toxin inhibits translation through ADP-ribosylation of EF-Tu P-loop.
Authors: Jurenas, D. / Rey, M. / Byrne, D. / Chamot-Rooke, J. / Terradot, L. / Cascales, E.
History
DepositionApr 6, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 18, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jun 19, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RHS repeat protein
B: RHS repeat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0577
Polymers24,7302
Non-polymers3275
Water66737
1
A: RHS repeat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6926
Polymers12,3651
Non-polymers3275
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RHS repeat protein


Theoretical massNumber of molelcules
Total (without water)12,3651
Polymers12,3651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.546, 66.366, 67.700
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LYS / End label comp-ID: LYS / Auth seq-ID: 1 - 113 / Label seq-ID: 3 - 115

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB

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Components

#1: Protein RHS repeat protein


Mass: 12364.904 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: D5823_18215, G0J71_10035, G0K31_21120 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A3Y4SQA0
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


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

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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: 2.34 Å3/Da / Density % sol: 47.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Zinc acetate dihydrate, 0.1 M Sodium cacodylate trihydrate pH 6.5, 18% w/v Polyethylene glycol 8,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 1.27819 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.27819 Å / Relative weight: 1
ReflectionResolution: 2.2→47.392 Å / Num. obs: 12221 / % possible obs: 99.3 % / Redundancy: 36.8 % / Biso Wilson estimate: 35.26 Å2 / Rpim(I) all: 0.035 / Rrim(I) all: 0.212 / Rsym value: 0.205 / Net I/av σ(I): 2.8 / Net I/σ(I): 15.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.2-2.3237.91.4330.56522417210.2351.4611.4335.798.7
2.32-2.4636.41.0670.66018316530.1791.0891.067798.4
2.46-2.6337.50.8020.85845815570.1320.8180.8028.899.4
2.63-2.8438.30.5691.15593914590.0930.5810.56910.899.6
2.84-3.1137.80.3561.75058613380.0590.3640.35614.199.4
3.11-3.48360.2182.74437012330.0370.2240.21818.599.7
3.48-4.0235.40.1364.43928511100.0230.140.1362599.9
4.02-4.9235.80.1075.4336989420.0180.110.10730.699.9
4.92-6.9636.20.0936.3271917510.0160.0990.09330.3100
6.96-41.01232.60.0876.9148864570.0160.0930.08732.999.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
SCALAdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→41.012 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2258 510 4.19 %random
Rwork0.192 11666 --
obs0.1935 12176 99.06 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 124.09 Å2 / Biso mean: 35.5685 Å2 / Biso min: 11.26 Å2
Refinement stepCycle: final / Resolution: 2.2→41.012 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1666 0 5 37 1708
Biso mean--79.55 33.37 -
Num. residues----225
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011699
X-RAY DIFFRACTIONf_angle_d1.2212310
X-RAY DIFFRACTIONf_chiral_restr0.051260
X-RAY DIFFRACTIONf_plane_restr0.008304
X-RAY DIFFRACTIONf_dihedral_angle_d15.271620
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A909X-RAY DIFFRACTION11.242TORSIONAL
12B909X-RAY DIFFRACTION11.242TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2001-2.42150.29211380.2271281898
2.4215-2.77180.2806900.2155288599
2.7718-3.49190.26361350.2051292199
3.4919-41.010.18731470.17143042100
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)
10.00990.0007-0.0089-0.00120.0060.0142-0.0715-0.01460.07960.1893-0.0221-0.00080.05860.088600.2143-0.01010.03180.2019-0.00010.220839.316422.717348.3925
20.0043-0.0003-0.00610.00090.00430.00390.034-0.08220.10180.1238-0.0152-0.1038-0.1156-0.029400.2216-0.00720.01780.16480.01670.24944.682233.678647.7915
30.0047-0.00520-0.0017-0.00170.0011-0.0105-0.01340.03420.0386-0.0197-0.03210.05940.1500.1976-0.0158-0.00130.26970.05170.200937.591532.374555.484
40.00750.0056-0.00190.0064-0.01010.0115-0.0056-0.0094-0.0331-0.02690.0443-0.01150.0155-0.032900.2241-0.0325-0.0010.2105-0.0190.210634.304420.559550.3801
50.00850.0001-0.00330.0042-0.00130.0067-0.01660.01350.0819-0.0320.04530.01830.0652-0.010100.2827-0.07390.00750.4685-0.05450.272731.27620.366141.3338
60.01550.04980.00920.025-0.00210.02820.08990.0581-0.0186-0.09710.09120.00040.0148-0.028800.19510.009-0.02020.21440.0350.213537.50224.62846.7093
70.0041000.0038-0.00040.00140.016-0.1041-0.02960.02440.0582-0.0070.0398-0.032900.4376-0.0853-0.04020.3590.02850.341329.12617.805156.3012
80.0094-0.0058-0.00270.00350.0115-0.0024-0.01090.07620.01450.1321-0.01820.0044-0.05820.0292-00.2283-0.04490.03760.1833-0.02150.242233.892128.203860.2912
90.00820.00950.0020.0107-0.00510.003-0.0012-0.02430.05640.0378-0.08550.0035-0.106-0.0132-00.25370.0033-0.02540.2693-0.02080.204929.733330.815269.0477
10-0.0202-0.0025-0.0279-0.0098-0.0071-0.00040.05490.0908-0.05860.19740.1108-0.21620.02640.0871-00.26820.04190.01770.29180.00070.242341.564226.228761.6369
110.00610.0075-0.00290.00920.00140.00630.05030.0782-0.12880.01380.0646-0.1687-0.0435-0.0874-00.3245-0.10390.05130.5815-0.02220.089239.331125.657236.9616
12-0.003-0.00750.0098-0.00730.0120.0106-0.01540.03930.147-0.04980.03940.03420.04410.0124-00.3772-0.3350.22090.5862-0.0597-0.529735.103324.804331.8177
130.01830.0179-0.00330.00370.01840.0298-0.0932-0.13550.03310.39150.12010.0099-0.0378-0.1236-00.19360.01860.00730.125-0.01320.204610.728717.487954.2367
140.00590.0257-0.00460.00360.01640.0018-0.1168-0.19610.01180.13770.05350.0866-0.06130.1073-00.2226-0.0032-0.00770.1892-0.00950.203817.39622.487757.875
150.0032-0.0083-0.00540.00150.00890.0098-0.01590.0974-0.011-0.04140.0496-0.1316-0.00330.0719-00.246-0.0462-0.02770.2757-0.01150.29120.864317.475544.5175
160.00840.0053-0.01710.00480.00370.01290.04480.03750.1518-0.0982-0.00640.10360.0323-0.0317-00.1892-0.0135-0.02780.21850.01090.23510.69124.150751.6221
170.0123-0.00390.00080.01060.02260.0072-0.0885-0.0771-0.00350.0797-0.13880.00710.0302-0.011300.27390.0064-0.00160.1935-0.01490.328919.796928.64457.0831
180.0317-0.025-0.02590.0277-0.00110.00830.0605-0.11140.05860.0243-0.07070.1464-0.1304-0.0643-00.2464-0.0482-0.01420.3203-0.04390.247914.974828.415966.5687
190.00650.0083-0.0054-0.0016-0.00280.00920.00610.0510.1956-0.0445-0.00770.20820.0062-0.048100.2579-0.01080.00010.2007-0.07840.247212.638412.716944.0284
200.0014-0.00120.00120.00170.00470.0066-0.0930.0212-0.0074-0.0617-0.04080.15220.0187-0.0059-00.2877-0.0087-0.00240.228-0.03040.271717.29439.59739.293
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 10 )A1 - 10
2X-RAY DIFFRACTION2chain 'A' and (resid 11 through 20 )A11 - 20
3X-RAY DIFFRACTION3chain 'A' and (resid 21 through 29 )A21 - 29
4X-RAY DIFFRACTION4chain 'A' and (resid 30 through 38 )A30 - 38
5X-RAY DIFFRACTION5chain 'A' and (resid 39 through 43 )A39 - 43
6X-RAY DIFFRACTION6chain 'A' and (resid 44 through 61 )A44 - 61
7X-RAY DIFFRACTION7chain 'A' and (resid 62 through 69 )A62 - 69
8X-RAY DIFFRACTION8chain 'A' and (resid 70 through 77 )A70 - 77
9X-RAY DIFFRACTION9chain 'A' and (resid 78 through 85 )A78 - 85
10X-RAY DIFFRACTION10chain 'A' and (resid 86 through 99 )A86 - 99
11X-RAY DIFFRACTION11chain 'A' and (resid 100 through 106 )A100 - 106
12X-RAY DIFFRACTION12chain 'A' and (resid 107 through 113 )A107 - 113
13X-RAY DIFFRACTION13chain 'B' and (resid 1 through 20 )B1 - 20
14X-RAY DIFFRACTION14chain 'B' and (resid 21 through 35 )B21 - 35
15X-RAY DIFFRACTION15chain 'B' and (resid 36 through 50 )B36 - 50
16X-RAY DIFFRACTION16chain 'B' and (resid 51 through 61 )B51 - 61
17X-RAY DIFFRACTION17chain 'B' and (resid 62 through 77 )B62 - 77
18X-RAY DIFFRACTION18chain 'B' and (resid 78 through 99 )B78 - 99
19X-RAY DIFFRACTION19chain 'B' and (resid 100 through 106 )B100 - 106
20X-RAY DIFFRACTION20chain 'B' and (resid 107 through 113 )B107 - 113

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