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- PDB-5ja9: Crystal structure of the HigB2 toxin in complex with Nb6 -

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Basic information

Entry
Database: PDB / ID: 5ja9
TitleCrystal structure of the HigB2 toxin in complex with Nb6
Components
  • Nanobody 6Single-domain antibody
  • Toxin HigB-2
KeywordsTOXIN / toxin-antitoxin system
Function / homologyToxin HigB-2 / RelE toxin of RelE / RelB toxin-antitoxin system / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Toxin HigB-2
Function and homology information
Biological speciesVibrio cholerae serotype O1 (bacteria)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.849 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
DepositionApr 12, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1May 17, 2017Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Toxin HigB-2
D: Toxin HigB-2
A: Nanobody 6
B: Nanobody 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,84412
Polymers53,1104
Non-polymers7358
Water2,774154
1
C: Toxin HigB-2
A: Nanobody 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0017
Polymers26,5552
Non-polymers4465
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-54 kcal/mol
Surface area11310 Å2
MethodPISA
2
D: Toxin HigB-2
B: Nanobody 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8435
Polymers26,5552
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-30 kcal/mol
Surface area11550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.760, 60.400, 88.590
Angle α, β, γ (deg.)90.000, 104.260, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and segid A
21chain B and segid B
12chain C and segid C
22chain D and segid D

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and segid AA0
211chain B and segid BB0
112chain C and segid CC0
212chain D and segid DD0

NCS ensembles :
ID
1
2

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Components

#1: Protein Toxin HigB-2


Mass: 13025.962 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) (bacteria)
Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: higB-2, VC_A0468 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KMA6
#2: Antibody Nanobody 6 / Single-domain antibody


Mass: 13528.946 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.25 Å3/Da / Density % sol: 45.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M Hepes pH 7.5, 10% (w/v) PEG8000, 8% (w/v) Ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97903 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.979031
ReflectionResolution: 1.849→49.404 Å / Num. obs: 38530 / % possible obs: 95.8 % / Observed criterion σ(I): -3 / Redundancy: 3.44 % / Biso Wilson estimate: 26.46 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.075 / Net I/σ(I): 10.27
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.85-1.960.950.93177.4
1.96-2.10.5061.98197.1
2.1-2.260.3443.51199.9
2.26-2.480.2464.81199.9
2.48-2.770.1427.69199.8
2.77-3.20.08213.34199.7
3.2-3.910.04324.89199.7
3.91-5.520.03135.34199.8
5.52-49.4040.02535.77199.5

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.849→44.35 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.11
RfactorNum. reflection% reflection
Rfree0.2405 1916 4.99 %
Rwork0.1952 --
obs0.1975 38387 95.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 156.8 Å2 / Biso mean: 53.2997 Å2 / Biso min: 17.04 Å2
Refinement stepCycle: final / Resolution: 1.849→44.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3522 0 45 154 3721
Biso mean--107.06 46.02 -
Num. residues----446
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083722
X-RAY DIFFRACTIONf_angle_d1.0225037
X-RAY DIFFRACTIONf_chiral_restr0.046529
X-RAY DIFFRACTIONf_plane_restr0.005654
X-RAY DIFFRACTIONf_dihedral_angle_d12.7351328
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1056X-RAY DIFFRACTION9.622TORSIONAL
12B1056X-RAY DIFFRACTION9.622TORSIONAL
21C917X-RAY DIFFRACTION9.622TORSIONAL
22D917X-RAY DIFFRACTION9.622TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8489-1.89510.3698990.39371896199570
1.8951-1.94640.36261140.34692205231982
1.9464-2.00360.31300.2962459258991
2.0036-2.06830.30911420.27162689283199
2.0683-2.14220.24361420.25032689283199
2.1422-2.2280.30511430.220527142857100
2.228-2.32940.28011420.209627032845100
2.3294-2.45220.27531420.213626982840100
2.4522-2.60580.24311420.20892713285599
2.6058-2.8070.27091420.20382709285199
2.807-3.08940.26031430.194427222865100
3.0894-3.53630.23741440.176327412885100
3.5363-4.45470.19191450.149427512896100
4.4547-44.36280.19551460.16042782292899
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)
14.43091.6523-0.87444.0863-2.03137.002-0.08891.10550.0056-0.3728-0.0891-0.5092-0.30070.86460.08930.4408-0.050.03640.64570.0430.3215-0.267832.7941-31.4919
26.54041.0849-0.07253.877-1.77852.2611-0.31730.76030.0912-0.3413-0.0346-0.4471-0.34920.3680.28160.5099-0.04810.02910.6754-0.03720.3190.74312.9851-32.6512
33.64471.1147-0.11441.29260.15291.8654-0.03890.05080.0654-0.0799-0.02540.1305-0.0657-0.0530.05990.28740.01210.00810.0835-0.00620.2749-14.336428.6783-8.2417
43.53010.70610.29772.1141-0.42061.5394-0.0120.1516-0.1744-0.06890.1220.03520.1-0.0162-0.09520.30150.04620.01360.1186-0.02580.2787-12.8517-0.7143-10.0424
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'C' and (resid 2 through 109 )C2 - 109
2X-RAY DIFFRACTION2chain 'D' and (resid 2 through 109 )D2 - 109
3X-RAY DIFFRACTION3chain 'A' and (resid 2 through 124 )A2 - 124
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 124 )B2 - 124

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