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- PDB-4fxh: Crystal structure of the isolated E. coli RelE toxin, P212121 form -

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Basic information

Entry
Database: PDB / ID: 4fxh
TitleCrystal structure of the isolated E. coli RelE toxin, P212121 form
ComponentsmRNA interferase RelE
KeywordsTOXIN / toxin/antitoxin system / nuclease / translational control / stress response / RelB / Ribosome / B-ME on Cys50
Function / homology
Function and homology information


toxin sequestering activity / toxin-antitoxin complex / single-species biofilm formation / regulation of growth / DNA-binding transcription repressor activity / mRNA catabolic process / RNA endonuclease activity / cellular response to amino acid starvation / protein-DNA complex / ribosome binding ...toxin sequestering activity / toxin-antitoxin complex / single-species biofilm formation / regulation of growth / DNA-binding transcription repressor activity / mRNA catabolic process / RNA endonuclease activity / cellular response to amino acid starvation / protein-DNA complex / ribosome binding / negative regulation of translation / Hydrolases; Acting on ester bonds / rRNA binding / transcription cis-regulatory region binding / response to antibiotic / regulation of DNA-templated transcription
Similarity search - Function
ParE toxin of type II toxin-antitoxin system, parDE / Toxin-antitoxin system, RelE/ParE toxin family / RelE-like / YaeB-like fold / Toxin-antitoxin system, RelE/ParE toxin domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
mRNA interferase toxin RelE
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBrodersen, D.E. / Boggild, A. / Sofos, N.
CitationJournal: Structure / Year: 2012
Title: The crystal structure of the intact E. coli RelBE toxin-antitoxin complex provides the structural basis for conditional cooperativity.
Authors: Boggild, A. / Sofos, N. / Andersen, K.R. / Feddersen, A. / Easter, A.D. / Passmore, L.A. / Brodersen, D.E.
History
DepositionJul 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2012Group: Database references
Revision 1.2Sep 13, 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 / diffrn_source / pdbx_initial_refinement_model / struct_conn / 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 / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: mRNA interferase RelE
B: mRNA interferase RelE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5693
Polymers22,4732
Non-polymers961
Water3,495194
1
A: mRNA interferase RelE


Theoretical massNumber of molelcules
Total (without water)11,2361
Polymers11,2361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: mRNA interferase RelE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3322
Polymers11,2361
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-7 kcal/mol
Surface area11140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.631, 61.443, 63.904
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein mRNA interferase RelE / Endoribonuclease RelE / Toxin RelE


Mass: 11236.251 Da / Num. of mol.: 2 / Fragment: RelE / Mutation: R81A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b1563, JW1555, relE / Plasmid: pSC2524HE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P0C077, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O

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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: 2.04 Å3/Da / Density % sol: 39.61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES, 0.2 M ammonium sulphate, 30% PEG 5000 MME, pH 6.5, vapor diffusion, sitting drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.91838 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 6, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91838 Å / Relative weight: 1
ReflectionResolution: 2.3→44.291 Å / Num. all: 8223 / Num. obs: 8223 / % possible obs: 96.8 % / Redundancy: 4.1 % / Biso Wilson estimate: 40.7 Å2 / Rsym value: 0.049 / Net I/σ(I): 18.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.3-2.364.10.1515.124846010.15198
2.36-2.424.10.1345.724435900.13497.8
2.42-2.494.10.1166.623915790.11698.2
2.49-2.574.10.1037.323475750.10398.1
2.57-2.664.20.0928.321995210.09296.4
2.66-2.754.10.0819.521135160.08197.3
2.75-2.854.20.06910.421225060.06997.4
2.85-2.974.10.06111.619904850.06197.1
2.97-3.14.20.04913.219344650.04996.4
3.1-3.254.20.04714.318494440.04797.6
3.25-3.434.20.04114.617694230.04196.4
3.43-3.644.10.04513.716624020.04596.3
3.64-3.894.10.0491315663790.04996.3
3.89-4.24.20.05111.614563500.05196.9
4.2-4.64.10.0511.613613300.0596.3
4.6-5.144.10.04214.712232980.04295.5
5.14-5.944.10.03815.110662630.03895.6
5.94-7.274.10.03513.79072200.03595
7.27-10.2940.02817.56891730.02892.4
10.29-44.2913.70.02819.13761030.02887.6

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3KHA

3kha
PDB Unreleased entry


Resolution: 2.4→37.669 Å / Occupancy max: 1 / Occupancy min: 0.35 / FOM work R set: 0.7941 / SU ML: 0.39 / σ(F): 1.39 / Phase error: 26.7
RfactorNum. reflection% reflectionSelection details
Rfree0.2822 350 4.85 %Random
Rwork0.2357 ---
obs0.238 7220 95.26 %-
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.36 Å2 / ksol: 0.323 e/Å3
Displacement parametersBiso max: 119.39 Å2 / Biso mean: 47.4198 Å2 / Biso min: 5.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.5881 Å20 Å2-0 Å2
2--0.6751 Å20 Å2
3----2.2632 Å2
Refinement stepCycle: LAST / Resolution: 2.4→37.669 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1513 0 5 194 1712
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041551
X-RAY DIFFRACTIONf_angle_d0.8272077
X-RAY DIFFRACTIONf_chiral_restr0.057232
X-RAY DIFFRACTIONf_plane_restr0.004257
X-RAY DIFFRACTIONf_dihedral_angle_d20.435629
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
2.4-2.74720.3341190.286422612380226197
2.7472-3.46080.33941210.243922882409228896
3.4608-37.67330.23661100.215923212431232193
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)
16.1785-0.1694-1.01644.7509-1.1972.0919-0.17630.64690.0696-0.43520.1090.2948-0.0759-0.16880.00490.40510.0643-0.15910.1905-0.03080.2756-0.2722-15.2763-15.8531
24.9195-2.84663.80733.7407-2.48987.81050.2948-0.003-1.2397-0.20411.17681.39191.4535-0.7995-1.28480.5613-0.13580.09160.62860.16270.8647-3.11-24.8727-10.5237
36.4759-0.27290.89526.350.82156.2504-0.2854-0.54540.18940.51430.3856-0.60090.00930.239-0.09050.18980.08570.01870.3132-0.0370.21467.5281-14.1397-7.1067
44.2331-1.35411.15057.1769-0.10264.59580.98360.2072-0.5695-0.0171-0.0026-0.86870.50290.0989-0.74630.38070.34380.21271.0525-0.43320.957110.9152-31.6435-16.5502
52.2074-1.20381.194.84890.28022.1137-0.20080.29660.2268-0.27680.38240.1547-0.10440.61950.02840.2794-0.0274-0.02770.3108-0.03510.43019.5401-43.1749-18.7901
63.7981-1.003-1.76981.9865-2.08024.57930.82771.0512-0.8271-0.24410.7939-0.46770.37440.3353-0.6883-0.84670.737-0.13880.6087-0.7771.754523.5555-47.7149-13.1021
72.03316.43035.32998.73817.60862.0281-0.81990.89790.7391-1.55820.35090.5066-0.82751.86960.40480.7389-0.06340.12630.4589-0.05770.391624.7341-35.453-18.1848
85.52472.35382.85942.7422-0.0882.4442-0.72770.67780.1041-0.86190.43-0.78980.04210.738-0.05371.00380.39230.16991.1928-0.25660.698332.4571-30.5592-10.9531
97.46451.1032-0.54667.68822.24433.73550.4118-0.1224-1.08981.3820.7203-1.9784-0.27461.4865-0.9640.7023-0.0577-0.33750.5499-0.07970.492428.8831-39.0321-4.347
106.32480.7189-0.84592.046-1.03760.87821.3321-1.7769-1.47340.957-0.03020.02870.2678-0.5525-0.90390.896-0.0522-0.2180.62740.10130.62918.6732-46.889-1.1686
119.68221.7392-3.88592.15730.17925.88080.0518-1.35780.23640.3915-0.81711.4313-0.7841-2.96631.23130.70860.10190.03240.7084-0.18880.46269.5187-41.2763-7.2572
127.43157.06990.37062.0139-2.98263.48411.3328-0.89840.78131.9615-0.22891.2666-0.1608-0.4498-0.73310.4738-0.12490.09340.5726-0.16450.309221.5072-31.8588-1.7482
132.4686.08520.52758.8456-0.7755.73930.3721-0.0924-0.7712-0.4614-0.3975-0.55340.6811-0.61870.06260.38420.0455-0.10180.4173-0.0410.346717.3374-43.7751-10.1267
144.963-1.12640.46257.93772.60364.88320.03130.04670.3292-0.69320.1842-0.766-0.1572-0.3936-0.05450.25830.0803-0.02350.3083-0.0730.194319.5365-35.5908-12.1892
156.65615.6108-0.36032.036-6.28456.9735-0.00640.7685-0.4186-0.1454-0.6416-1.19250.15780.30010.50340.36740.17110.00290.65110.00210.250312.7825-17.6509-18.1793
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 2:15)A2 - 15
2X-RAY DIFFRACTION2chain 'A' and (resseq 16:33)A16 - 33
3X-RAY DIFFRACTION3chain 'A' and (resseq 34:78)A34 - 78
4X-RAY DIFFRACTION4chain 'A' and (resseq 79:83)A79 - 83
5X-RAY DIFFRACTION5chain 'A' and (resseq 84:95)A84 - 95
6X-RAY DIFFRACTION6chain 'B' and (resseq 2:8)B2 - 8
7X-RAY DIFFRACTION7chain 'B' and (resseq 9:15)B9 - 15
8X-RAY DIFFRACTION8chain 'B' and (resseq 16:21)B16 - 21
9X-RAY DIFFRACTION9chain 'B' and (resseq 22:33)B22 - 33
10X-RAY DIFFRACTION10chain 'B' and (resseq 34:42)B34 - 42
11X-RAY DIFFRACTION11chain 'B' and (resseq 43:51)B43 - 51
12X-RAY DIFFRACTION12chain 'B' and (resseq 52:59)B52 - 59
13X-RAY DIFFRACTION13chain 'B' and (resseq 60:70)B60 - 70
14X-RAY DIFFRACTION14chain 'B' and (resseq 71:84)B71 - 84
15X-RAY DIFFRACTION15chain 'B' and (resseq 85:95)B85 - 95

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