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- PDB-3bpq: Crystal Structure of RelB-RelE antitoxin-toxin complex from Metha... -

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Basic information

Entry
Database: PDB / ID: 3bpq
TitleCrystal Structure of RelB-RelE antitoxin-toxin complex from Methanococcus jannaschii
Components
  • Antitoxin RelB3
  • Toxin RelE3
KeywordsTOXIN / protein toxin-antitoxin complex
Function / homology
Function and homology information


nuclease activity / Hydrolases; Acting on ester bonds
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2100 / : / RelB Antitoxin / : / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2100 / : / RelB Antitoxin / : / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Antitoxin RelB3 / Toxin RelE3
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.2 Å
AuthorsFrancuski, D. / Saenger, W.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Crystal structure of the antitoxin-toxin protein complex RelB-RelE from Methanococcus jannaschii
Authors: Francuski, D. / Saenger, W.
History
DepositionDec 19, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 24, 2011Group: Database references / Source and taxonomy
Revision 1.3Aug 31, 2011Group: Database references / Structure summary
Revision 1.4Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Antitoxin RelB3
B: Toxin RelE3
C: Antitoxin RelB3
D: Toxin RelE3


Theoretical massNumber of molelcules
Total (without water)33,6784
Polymers33,6784
Non-polymers00
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7610 Å2
ΔGint-52 kcal/mol
Surface area14260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.794, 57.992, 58.747
Angle α, β, γ (deg.)90.00, 92.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Antitoxin RelB3 / RelB


Mass: 6323.375 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Strain: DSM2661 / Gene: relB3, relB, MJ1103.1 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): K-12 / References: UniProt: P0CL56
#2: Protein Toxin RelE3 / Uncharacterized protein MJ1103 / MjRelE / Putative endoribonuclease RelE


Mass: 10515.409 Da / Num. of mol.: 2 / Mutation: R62S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Strain: DSM2661 / Gene: MJ1103, relE, relE3 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): K-12
References: UniProt: Q58503, Hydrolases; Acting on ester bonds
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.67 Å3/Da / Density % sol: 53.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 20%MPD, 0.1M Bis-Tris pH5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.94905 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 12, 2006 / Details: mirrors
RadiationMonochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94905 Å / Relative weight: 1
ReflectionResolution: 2.13→50 Å / Num. obs: 19952 / % possible obs: 99.6 % / Observed criterion σ(I): 3 / Redundancy: 4.2 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.4
Reflection shellResolution: 2.13→2.18 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.421 / Mean I/σ(I) obs: 3.13 / Num. unique all: 1332 / % possible all: 98.9

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Phasing

PhasingMethod: MIR
Phasing set
ID
1
2
3
Phasing MIR der

Native set-ID: 1 / Resolution: 2.13→32.95 Å

IDR cullis acentricR cullis centricDer set-IDReflection acentricReflection centric
ISO_100118691951
ISO_20.8420.794210255302
ISO_30.9070.79238870271
Phasing MIR der shell
Highest resolution (Å)Lowest resolution (Å)Der-IDR cullis acentricR cullis centricReflection acentricReflection centric
9.1732.95ISO_10016636
6.619.17ISO_10037246
5.446.61ISO_10049156
4.725.44ISO_10058953
4.234.72ISO_10065647
3.874.23ISO_10072546
3.593.87ISO_10079741
3.363.59ISO_10086434
3.173.36ISO_10090445
3.013.17ISO_10096343
2.873.01ISO_100101549
2.752.87ISO_100106050
2.642.75ISO_100110944
2.542.64ISO_100114051
2.462.54ISO_100122351
2.382.46ISO_100123854
2.312.38ISO_100127651
2.242.31ISO_100132557
2.192.24ISO_100137754
2.132.19ISO_100140143
9.1732.95ISO_20.6730.73216518
6.619.17ISO_20.740.71237221
5.446.61ISO_20.7780.72449130
4.725.44ISO_20.8030.87558925
4.234.72ISO_20.8720.865626
3.874.23ISO_20.9030.76572520
3.593.87ISO_20.8870.80379519
3.363.59ISO_20.8760.92186415
3.173.36ISO_20.8731.00590422
3.013.17ISO_20.9030.84596224
2.873.01ISO_20.9020.966101424
2.752.87ISO_20.8851.169105923
2.642.75ISO_20.9421.002110825
2.542.64ISO_20.9671.65855110
2.462.54ISO_20000
2.382.46ISO_20000
2.312.38ISO_20000
2.242.31ISO_20000
2.192.24ISO_20000
2.132.19ISO_20000
9.1732.95ISO_30.7590.63716518
6.619.17ISO_30.8210.93137222
5.446.61ISO_30.8430.86949130
4.725.44ISO_30.9320.90658825
4.234.72ISO_30.940.75765326
3.874.23ISO_30.951.03972521
3.593.87ISO_30.9420.90279719
3.363.59ISO_30.9540.87786416
3.173.36ISO_30.9740.9590221
3.013.17ISO_31.0021.37196124
2.873.01ISO_30.9930.844101424
2.752.87ISO_31.0421.099104622
2.642.75ISO_31.0250.7752923
2.542.64ISO_30000
2.462.54ISO_30000
2.382.46ISO_30000
2.312.38ISO_30000
2.242.31ISO_30000
2.192.24ISO_30000
2.132.19ISO_30000

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345data collection
HKL-2000data reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MIR / Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.903 / SU B: 16.068 / SU ML: 0.202 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.273 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27418 931 5.1 %RANDOM
Rwork0.23825 ---
obs0.24007 17159 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.042 Å2
Baniso -1Baniso -2Baniso -3
1-0.73 Å20 Å23.78 Å2
2---3.96 Å20 Å2
3---3.53 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2118 0 0 56 2174
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222173
X-RAY DIFFRACTIONr_angle_refined_deg1.0581.9772908
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2175252
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.57123.704108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.515452
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4871516
X-RAY DIFFRACTIONr_chiral_restr0.0740.2318
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021584
X-RAY DIFFRACTIONr_nbd_refined0.1980.2909
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21446
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.296
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1610.216
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0940.28
X-RAY DIFFRACTIONr_mcbond_it0.3881.51310
X-RAY DIFFRACTIONr_mcangle_it0.66122039
X-RAY DIFFRACTIONr_scbond_it0.9613980
X-RAY DIFFRACTIONr_scangle_it1.4034.5866
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 70 -
Rwork0.268 1242 -
obs--100 %
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)
18.89292.5767-6.65657.3312-5.4511.3070.62490.5360.26070.5088-0.190.296-0.82160.1877-0.4348-0.16670.008-0.0289-0.1954-0.0559-0.0188-2.29939.96623.113
26.41521.5309-1.56027.8828-0.2775.3240.00780.3770.07360.1306-0.0070.9151-0.0205-0.3079-0.0009-0.19920.025-0.0023-0.2159-0.0205-0.0205-9.31941.50526.466
310.3537-12.1209-8.964420.417512.705611.27470.41760.26880.538-0.83230.0404-0.7986-0.5259-0.201-0.4579-0.2091-0.04020.0383-0.0279-0.019-0.114516.67633.29510.017
45.05980.1154-0.41118.88841.25096.33620.04420.10270.2956-0.40030.1466-0.464-0.01050.1377-0.1908-0.2008-0.04230.06020.0047-0.0787-0.116623.54932.2216.211
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA8 - 488 - 48
2X-RAY DIFFRACTION2BB3 - 883 - 88
3X-RAY DIFFRACTION3CC9 - 479 - 47
4X-RAY DIFFRACTION4DD3 - 883 - 88

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