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- PDB-5i4q: Contact-dependent inhibition system from Escherichia coli NC101 -... -

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Basic information

Entry
Database: PDB / ID: 5i4q
TitleContact-dependent inhibition system from Escherichia coli NC101 - ternary CdiA/CdiI/EF-Tu complex (domains 2 and 3)
Components
  • (Contact-dependent inhibitor ...) x 2
  • Elongation factor Tu
KeywordsTOXIN/ANTITOXIN / toxin / antitoxin / elongation factor / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / Structure-Function Analysis of Polymorphic CDI Toxin-Immunity Protein Complexes / UC4CDI / TOXIN-ANTITOXIN complex
Function / homology
Function and homology information


guanyl-nucleotide exchange factor complex / protein-synthesizing GTPase / guanosine tetraphosphate binding / translational elongation / translation elongation factor activity / toxin activity / endonuclease activity / Hydrolases; Acting on ester bonds / response to antibiotic / GTPase activity ...guanyl-nucleotide exchange factor complex / protein-synthesizing GTPase / guanosine tetraphosphate binding / translational elongation / translation elongation factor activity / toxin activity / endonuclease activity / Hydrolases; Acting on ester bonds / response to antibiotic / GTPase activity / GTP binding / magnesium ion binding / RNA binding / extracellular region / plasma membrane / cytoplasm
Similarity search - Function
: / : / Family of unknown function (DUF6862) / Toxin CdiA-like, Filamentous hemagglutinin motif repeats / VENN motif-containing domain / Pre-toxin domain with VENN motif / Hemagglutinin repeat / Hemagglutinin repeat / Filamentous haemagglutinin FhaB/tRNA nuclease CdiA-like, TPS domain / TPS secretion domain ...: / : / Family of unknown function (DUF6862) / Toxin CdiA-like, Filamentous hemagglutinin motif repeats / VENN motif-containing domain / Pre-toxin domain with VENN motif / Hemagglutinin repeat / Hemagglutinin repeat / Filamentous haemagglutinin FhaB/tRNA nuclease CdiA-like, TPS domain / TPS secretion domain / haemagglutination activity domain / Parallel beta-helix repeat / Parallel beta-helix repeats / Translation elongation factor EFTu/EF1A, C-terminal / Translation elongation factor EFTu/EF1A, bacterial/organelle / Elongation factor Tu, domain 2 / Elongation factor Tu (EF-Tu), GTP-binding domain / : / Elongation factor Tu C-terminal domain / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Translation factors / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Pectin lyase fold / Pectin lyase fold/virulence factor / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Elongation Factor Tu (Ef-tu); domain 3 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Small GTP-binding protein domain / Translation protein, beta-barrel domain superfamily / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Elongation factor Tu / Elongation factor Tu 1 / tRNA nuclease CdiA / Immunity protein CdiI
Similarity search - Component
Biological speciesEscherichia coli NC101 (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.35 Å
AuthorsMichalska, K. / Stols, L. / Eschenfeldt, W. / Hayes, C.S. / Goulding, C.W. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) / Structure-Function Analysis of Polymorphic CDI Toxin-Immunity Protein Complexes (UC4CDI)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM094585 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM102318 United States
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: Structure of a novel antibacterial toxin that exploits elongation factor Tu to cleave specific transfer RNAs.
Authors: Michalska, K. / Gucinski, G.C. / Garza-Sanchez, F. / Johnson, P.M. / Stols, L.M. / Eschenfeldt, W.H. / Babnigg, G. / Low, D.A. / Goulding, C.W. / Joachimiak, A. / Hayes, C.S.
History
DepositionFeb 12, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.3Nov 8, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Contact-dependent inhibitor A
B: Contact-dependent inhibitor I
C: Elongation factor Tu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7535
Polymers48,6223
Non-polymers1322
Water1,65792
1
A: Contact-dependent inhibitor A
B: Contact-dependent inhibitor I
C: Elongation factor Tu
hetero molecules

A: Contact-dependent inhibitor A
B: Contact-dependent inhibitor I
C: Elongation factor Tu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,50610
Polymers97,2436
Non-polymers2634
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)131.155, 131.155, 63.327
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
DetailsHexamer according to size exclusion chromatography

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Components

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Contact-dependent inhibitor ... , 2 types, 2 molecules AB

#1: Protein Contact-dependent inhibitor A / CdiA


Mass: 10476.635 Da / Num. of mol.: 1 / Fragment: toxin domain
Source method: isolated from a genetically manipulated source
Details: The cloned fragment corresponds to Val3035-Lys3289 of the full-length protein (CdiA-CT). The final purified ternary complex was treated with trypsin that cleaved CdiA-CT after Lys3196.
Source: (gene. exp.) Escherichia coli NC101 (bacteria) / Strain: NC101 / Plasmid: pMCSG58 / Details (production host): dual expression vector / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Gold / References: UniProt: P0DSI1*PLUS
#2: Protein Contact-dependent inhibitor I / CdiI


Mass: 14227.428 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli NC101 (bacteria) / Strain: NC101 / Plasmid: pMCSG58 / Details (production host): dual expression vector / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Gold / References: UniProt: P0DSM8*PLUS

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Protein , 1 types, 1 molecules C

#3: Protein Elongation factor Tu / EF-Tu


Mass: 23917.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Trypsin treatment prior to crystallization cleaved EF-Tu after Lys177 or after Arg172, however subsequent digestion in situ cannot be excluded. The sample is a mixture of tufA and tufB gene ...Details: Trypsin treatment prior to crystallization cleaved EF-Tu after Lys177 or after Arg172, however subsequent digestion in situ cannot be excluded. The sample is a mixture of tufA and tufB gene products (GI 947838, 948482).
Source: (natural) Escherichia coli (E. coli) / References: UniProt: J7R9V6, UniProt: P0CE47*PLUS

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Non-polymers , 3 types, 94 molecules

#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.82 Å3/Da / Density % sol: 56.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M NaCl, 0.1 M Bis-Tris pH 6.5, 1.5 M ammonium sulfate, trypsin 40 ng/microL, cryo 28% sucrose

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 7, 2015 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.35→30 Å / Num. obs: 23688 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 9.1 % / Biso Wilson estimate: 37.2 Å2 / Rmerge(I) obs: 0.125 / Net I/σ(I): 20
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.953 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.35→30 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.945 / SU B: 12.941 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R: 0.245 / ESU R Free: 0.195 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21791 1125 4.8 %RANDOM
Rwork0.18142 ---
obs0.18322 22536 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 55.144 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20 Å20 Å2
2--0.38 Å20 Å2
3----0.76 Å2
Refinement stepCycle: 1 / Resolution: 2.35→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3061 0 6 92 3159
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0193134
X-RAY DIFFRACTIONr_bond_other_d0.0010.023021
X-RAY DIFFRACTIONr_angle_refined_deg1.6331.9764223
X-RAY DIFFRACTIONr_angle_other_deg1.36736967
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6655378
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.73823.311148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.74415549
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6261526
X-RAY DIFFRACTIONr_chiral_restr0.0940.2445
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213496
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02716
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.0973.2341521
X-RAY DIFFRACTIONr_mcbond_other3.0653.2331520
X-RAY DIFFRACTIONr_mcangle_it4.8034.8321896
X-RAY DIFFRACTIONr_mcangle_other4.8024.8341897
X-RAY DIFFRACTIONr_scbond_it4.553.8171613
X-RAY DIFFRACTIONr_scbond_other4.4843.7981609
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.1295.4242321
X-RAY DIFFRACTIONr_long_range_B_refined9.07825.3553383
X-RAY DIFFRACTIONr_long_range_B_other9.04425.283369
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.345→2.406 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 66 -
Rwork0.256 1568 -
obs--97.49 %
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)
10.56580.48692.49680.9021.562913.08790.0753-0.06060.0790.08330.09660.2948-0.0653-0.5075-0.17180.16370.07810.01370.1863-0.02530.27-8.682446.22862.2072
25.1032-1.6581-1.66941.8116-1.45463.69290.1067-0.1174-0.00480.16190.09630.1053-0.3251-0.0496-0.2030.14520.06550.00770.2509-0.11540.2067-4.146839.862311.0969
39.8108-2.30890.29871.5616-0.47130.172-0.1064-0.2670.009-0.11440.18250.17750.0632-0.0175-0.07610.13390.0276-0.01050.3124-0.0690.14122.243134.70345.5807
41.82050.821-0.04051.1572-0.13222.5512-0.0068-0.31470.3484-0.2767-0.08540.32040.1501-0.1710.09220.1044-0.0137-0.03830.3595-0.04080.1526-11.447326.1038.7946
50.10740.0141-0.54110.0099-0.09116.97160.0168-0.1229-0.0627-0.0266-0.01940.0045-0.0941-0.10240.00250.1115-0.0063-0.01540.3946-0.00490.1898-9.824925.129410.5406
62.7646-1.1379-1.43721.87491.45531.57570.2006-0.25940.04840.0222-0.1518-0.13590.1977-0.3472-0.04880.2653-0.16660.00530.5544-0.00930.0584-6.929626.69111.053
72.8353-1.2777-1.11490.58290.646310.85810.00950.0291-0.0524-0.0413-0.01810.017-0.31610.23960.00860.23620.00650.02960.12510.00320.164930.244521.1998-11.4942
84.9609-1.1478-6.21070.30671.43537.8157-0.0781-0.42220.0168-0.07050.1042-0.02370.04270.4207-0.02610.24710.09030.00970.33820.01480.107224.037319.99388.3476
92.3475-0.9799-1.34030.6509-0.23153.43390.0407-0.23250.0833-0.0117-0.0033-0.0398-0.0170.26-0.03730.1198-0.037-0.02620.4811-0.01880.01049.33124.218827.8988
102.9638-0.084-1.69830.46680.32421.2165-0.043-0.1364-0.1236-0.0122-0.033-0.08080.0842-0.05630.0760.14460.02860.01820.3712-0.00910.09297.396623.099312.9241
117.1827-2.97170.90592.0522-2.65516.441-0.0002-0.2635-0.7079-0.20270.17090.32010.546-0.2607-0.17070.1452-0.03920.01510.32650.02420.1051.671417.967726.1211
121.4064-0.4969-1.05370.96840.20192.0362-0.06350.13220.2207-0.00840.0980.06640.1259-0.1263-0.03450.15270.0101-0.06420.2252-0.0030.18112.792436.3998-9.433
132.34951.99230.71021.74910.55951.4384-0.0960.2947-0.2021-0.10550.3811-0.24510.06130.0759-0.28510.1027-0.02560.0450.2847-0.16820.237330.431939.326-17.5154
143.1823-0.0911-0.30923.154-0.32010.9778-0.0508-0.11860.5463-0.11820.3745-0.1432-0.06360.0635-0.32370.067-0.04740.03720.1328-0.07850.254924.89542.3388-15.7759
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A168 - 176
2X-RAY DIFFRACTION2A177 - 195
3X-RAY DIFFRACTION3A196 - 204
4X-RAY DIFFRACTION4A205 - 225
5X-RAY DIFFRACTION5A226 - 238
6X-RAY DIFFRACTION6A239 - 255
7X-RAY DIFFRACTION7B1 - 12
8X-RAY DIFFRACTION8B13 - 28
9X-RAY DIFFRACTION9B29 - 56
10X-RAY DIFFRACTION10B57 - 90
11X-RAY DIFFRACTION11B91 - 107
12X-RAY DIFFRACTION12C209 - 299
13X-RAY DIFFRACTION13C300 - 369
14X-RAY DIFFRACTION14C370 - 394

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