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- PDB-4fxi: Crystal structure of the isolated E. coli RelE toxin, P21 form -

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Basic information

Entry
Database: PDB / ID: 4fxi
TitleCrystal structure of the isolated E. coli RelE toxin, P21 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 / Hydrolases; Acting on ester bonds / rRNA binding / negative regulation of translation / 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 / RelE-like / Toxin-antitoxin system, RelE/ParE toxin family / 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 / molecular replacement / Resolution: 1.8003 Å
AuthorsBrodersen, D.E. / Boggild, A. / Sofos, N.
Citation
Journal: 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.
#1: Journal: Cell(Cambridge,Mass.) / Year: 2009
Title: The structural basis for mRNA recognition and cleavage by the ribosome-dependent endonuclease RelE.
Authors: Neubauer, C. / Gao, Y.G. / Andersen, K.R. / Dunham, C.M. / Kelley, A.C. / Hentschel, J. / Gerdes, K. / Ramakrishnan, V. / Brodersen, D.E.
History
DepositionJul 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
SupersessionSep 12, 2012ID: 3KHA
Revision 1.1Sep 12, 2012Group: Database references
Revision 1.2Dec 26, 2012Group: Database references
Revision 1.3Sep 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 / 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 / _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
C: mRNA interferase RelE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2859
Polymers33,7093
Non-polymers5766
Water4,846269
1
A: 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
MethodPISA
2
B: mRNA interferase RelE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5244
Polymers11,2361
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: mRNA interferase RelE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4283
Polymers11,2361
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
B: mRNA interferase RelE
C: mRNA interferase RelE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9537
Polymers22,4732
Non-polymers4805
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-13 kcal/mol
Surface area11540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.570, 61.140, 70.350
Angle α, β, γ (deg.)90.000, 102.930, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 11236.251 Da / Num. of mol.: 3 / 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


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


Mass: 18.015 Da / Num. of mol.: 269 / 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: 2.65 Å3/Da / Density % sol: 53.53 %
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: ESRF / Beamline: ID29 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 24, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.8→45.6 Å / Num. all: 32745 / Num. obs: 32079 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 39.855 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 17.74
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.8-1.850.5992.198844236597.4
1.85-1.90.43738579225697.8
1.9-1.950.314.228542224997.5
1.95-2.010.1956.528254217598
2.01-2.080.1518.547924209098.4
2.08-2.150.11210.847715203997.7
2.15-2.230.09412.897578200198.9
2.23-2.320.07615.177146189498.4
2.32-2.430.06118.266892182798.7
2.43-2.550.05121.136595175098.4
2.55-2.680.04524.066301168098.8
2.68-2.850.04226.615920158798.8
2.85-3.040.03729.665497148298.3
3.04-3.290.03432.895086138898.4
3.29-3.60.03135.454661127899
3.6-4.030.0336.954172115998.8
4.03-4.650.02737.873618102098.6
4.65-5.690.02638.43317986998.1
5.69-8.050.02938.04243267497.7
8.050.02735.7792229675.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å41.49 Å
Translation2.5 Å41.49 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.3.0phasing
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3KHA

3kha
PDB Unreleased entry


Resolution: 1.8003→41.491 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8382 / SU ML: 0.22 / σ(F): 1.36 / Phase error: 23.56
RfactorNum. reflection% reflectionSelection details
Rfree0.2185 1635 5.1 %Random
Rwork0.1838 ---
obs0.1857 32078 98.03 %-
all-32745 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 165.46 Å2 / Biso mean: 44.7062 Å2 / Biso min: 17.06 Å2
Refinement stepCycle: LAST / Resolution: 1.8003→41.491 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2340 0 30 269 2639
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062397
X-RAY DIFFRACTIONf_angle_d1.0543210
X-RAY DIFFRACTIONf_chiral_restr0.078354
X-RAY DIFFRACTIONf_plane_restr0.005393
X-RAY DIFFRACTIONf_dihedral_angle_d14.932945
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
1.8003-1.85330.33971460.270725112657251197
1.8533-1.91310.32921430.24324892632248998
1.9131-1.98150.23931280.225125192647251998
1.9815-2.06090.25811470.202825122659251298
2.0609-2.15460.21781310.188925202651252098
2.1546-2.26820.25411240.193925922716259299
2.2682-2.41030.25821240.188425302654253099
2.4103-2.59640.21721260.190625632689256399
2.5964-2.85760.24271280.208125622690256299
2.8576-3.2710.21351500.194825572707255799
3.271-4.12050.21721430.16625732716257399
4.1205-41.50210.181450.16225152660251595
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)
11.14220.34240.16810.3940.13561.3144-0.0902-0.3175-0.154-0.18670.23040.32140.4837-0.99870.0050.3812-0.1022-0.00240.364-0.00940.271910.85128.734417.6601
21.26710.96420.17981.27551.06531.40910.2034-0.0335-0.08840.2477-0.2326-0.1254-0.04950.1189-00.1813-0.02850.00770.2742-0.03270.254919.964816.712118.3527
32.48080.38450.34990.07510.03370.0533-0.37650.15630.4463-0.2520.4057-0.2639-0.22840.03610.01770.2967-0.04580.04850.3055-0.13370.210418.01415.03231.1293
40.2778-0.0286-0.58240.4026-0.05841.0287-0.1708-0.0304-0.3118-0.07570.2442-0.4196-0.01350.3118-00.21480.01920.01710.35-0.08990.34122.400411.537512.5125
50.14520.0211-0.2740.4585-0.20870.93560.36750.1209-0.1225-0.9345-0.20620.05350.4978-0.17630.00340.26-0.00660.00920.2622-0.04210.199810.826814.299910.8466
60.29760.5505-0.45251.8699-1.38031.0284-0.1254-0.6988-0.81610.8836-0.3808-1.4451.24540.7446-0.09320.90270.08060.03130.7658-0.07270.859825.8599-0.05078.261
72.3482-0.71010.48360.2421-0.1230.12760.03761.0802-0.0506-0.1636-0.1813-0.40961.3810.7055-0.03910.5736-0.02410.04860.4383-0.09390.319314.78644.29535.1752
80.21-0.142-0.2940.69780.11131.0861-0.03070.38320.2203-0.4397-0.011-0.0199-0.37850.07190.00190.2848-0.0469-0.04170.29390.09020.320130.514941.55297.2119
90.33060.7883-0.14061.7414-0.00740.7758-0.0450.2216-0.2235-0.2312-0.0717-0.22240.2925-0.0329-0.00040.2430.04530.02320.29540.04770.265731.549430.37257.2932
100.9631-0.2177-0.74771.40750.74991.43350.19960.0050.08350.7517-0.573-0.4194-0.1153-0.0097-0.1930.2636-0.0375-0.04660.28270.07940.337729.93830.68617.902
110.83641.0627-0.62151.0698-0.34451.5040.1153-0.28490.07110.1095-0.0638-0.076-0.24410.13560.00240.12940.0299-0.01950.23350.02460.191827.975437.202212.027
120.62380.435-0.57550.2574-0.36940.45590.03490.56720.368-0.59240.2139-0.2862-0.62560.15940.0120.5559-0.07540.00630.39140.09730.354149.617521.732426.0955
131.71370.5055-0.35110.2577-0.02290.9762-0.1516-1.0817-0.41230.7575-0.0966-0.10830.25740.5805-0.08140.3842-0.0703-0.01710.29740.00690.271945.593317.072840.8983
140.22730.02050.02710.0649-0.040.0252-0.4488-0.261-0.05130.32430.26480.9422-0.111-0.55480.00020.43810.07790.0590.35740.02360.434834.727416.944140.1078
152.6591-0.62920.37930.6620.59882.3042-0.14720.4695-0.1096-0.3989-0.02910.0483-0.4591-0.0907-0.05630.33280.0034-0.04520.18250.02680.282640.997116.193229.8244
161.34551.59780.06152.26740.11152.72690.1099-0.3185-0.45091.5154-0.4618-0.2361-0.7645-0.2813-0.0750.4633-0.14480.02770.4754-0.00980.282634.178541.371820.7524
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 2:18)A2 - 18
2X-RAY DIFFRACTION2(chain A and resid 19:42)A19 - 42
3X-RAY DIFFRACTION3(chain A and resid 43:49)A43 - 49
4X-RAY DIFFRACTION4(chain A and resid 50:65)A50 - 65
5X-RAY DIFFRACTION5(chain A and resid 66:80)A66 - 80
6X-RAY DIFFRACTION6(chain A and resid 81:85)A81 - 85
7X-RAY DIFFRACTION7(chain A and resid 86:95)A86 - 95
8X-RAY DIFFRACTION8(chain B and resid 2:14)B2 - 14
9X-RAY DIFFRACTION9(chain B and resid 15:43)B15 - 43
10X-RAY DIFFRACTION10(chain B and resid 44:59)B44 - 59
11X-RAY DIFFRACTION11(chain B and resid 60:80)B60 - 80
12X-RAY DIFFRACTION12(chain B and resid 81:95)B81 - 95
13X-RAY DIFFRACTION13(chain C and resid 2:22)C2 - 22
14X-RAY DIFFRACTION14(chain C and resid 23:35)C23 - 35
15X-RAY DIFFRACTION15(chain C and resid 36:83)C36 - 83
16X-RAY DIFFRACTION16(chain C and resid 84:95)C84 - 95

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