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- PDB-5mje: Crystal structure of the HigB2 toxin in complex with Nb8 -

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Basic information

Entry
Database: PDB / ID: 5mje
TitleCrystal structure of the HigB2 toxin in complex with Nb8
Components
  • Cytotoxic translational repressor of toxin-antitoxin stability system
  • Nanobody 8
KeywordsTOXIN / toxin-antitoxin system
Function / homologyToxin HigB-2 / RelE toxin of RelE / RelB toxin-antitoxin system / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / DI(HYDROXYETHYL)ETHER / Cytotoxic translational repressor of toxin-antitoxin stability system / Toxin HigB-2
Function and homology information
Biological speciesVibrio cholerae (bacteria)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.599 Å
AuthorsHadzi, S. / Loris, R.
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: Ribosome-dependent Vibrio cholerae mRNAse HigB2 is regulated by a beta-strand sliding mechanism.
Authors: Hadzi, S. / Garcia-Pino, A. / Haesaerts, S. / Jurenas, D. / Gerdes, K. / Lah, J. / Loris, R.
History
DepositionNov 30, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1May 17, 2017Group: Database references
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3Apr 9, 2025Group: 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

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Assembly

Deposited unit
A: Cytotoxic translational repressor of toxin-antitoxin stability system
B: Nanobody 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6364
Polymers29,4342
Non-polymers2022
Water30617
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-16 kcal/mol
Surface area11590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.290, 36.570, 60.800
Angle α, β, γ (deg.)90.000, 104.050, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cytotoxic translational repressor of toxin-antitoxin stability system / Toxin HigB-2 / Uncharacterized protein


Mass: 15066.139 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria)
Gene: EN12_16040, ERS013138_03879, ERS013140_03929, ERS013166_04476, ERS013173_04173, ERS013186_03907, ERS013199_03648, ERS013200_04302, ERS013207_03773
Production host: Escherichia coli (E. coli) / References: UniProt: A0A085RXT0, UniProt: Q9KMA6*PLUS
#2: Antibody Nanobody 8


Mass: 14367.790 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O
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: 2.1 Å3/Da / Density % sol: 41.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M Ammonium sulfate; 0,1 M sodium acetate pH 4.6; 30% PEG monomethyl ether 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.979 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.599→46.5 Å / Num. obs: 7617 / % possible obs: 98 % / Redundancy: 2.52 % / Biso Wilson estimate: 42.44 Å2 / CC1/2: 0.98 / Net I/σ(I): 5.39

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.599→46.469 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 37.87
RfactorNum. reflection% reflection
Rfree0.2965 379 4.98 %
Rwork0.2271 --
obs0.2307 7605 97.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 170.34 Å2 / Biso mean: 59.5379 Å2 / Biso min: 19.75 Å2
Refinement stepCycle: final / Resolution: 2.599→46.469 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1808 0 12 17 1837
Biso mean--81.17 38.51 -
Num. residues----235
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071851
X-RAY DIFFRACTIONf_angle_d0.9542495
X-RAY DIFFRACTIONf_chiral_restr0.05271
X-RAY DIFFRACTIONf_plane_restr0.006323
X-RAY DIFFRACTIONf_dihedral_angle_d20.5141097
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5988-2.97480.40131220.32212331245397
2.9748-3.74770.30291260.23332424255099
3.7477-46.47660.25811310.19232471260298
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)
12.29330.28870.12422.0471-0.56110.6329-0.21110.26010.4168-1.65020.36452.0032-0.1096-0.12230.09320.6275-0.0124-0.43930.38640.0671.045437.534327.5276-47.3037
22.21020.89170.32414.4544-0.14610.73260.0172-0.23520.0194-0.37970.07170.81990.10250.0541-0.06060.20020.04210.01840.30630.01750.356153.199235.0406-33.5261
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -7 through 110 )A-7 - 110
2X-RAY DIFFRACTION2chain 'B' and (resid 3 through 126 )B3 - 126

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