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- PDB-5ja8: Crystal structure of the HigB2 toxin in complex with Nb2 -

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Basic information

Entry
Database: PDB / ID: 5ja8
TitleCrystal structure of the HigB2 toxin in complex with Nb2
Components
  • Nanobody 2
  • Toxin HigB-2
KeywordsTOXIN / toxin-antitoxin system
Function / homology
Function and homology information


Toxin HigB-2 / RelE toxin of RelE / RelB toxin-antitoxin system / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / 1,3-PROPANDIOL / PHOSPHATE ION / Toxin HigB-2
Similarity search - Component
Biological speciesVibrio cholerae serotype O1 (bacteria)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 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
Revision 1.2Feb 20, 2019Group: Advisory / Data collection / Derived calculations
Category: diffrn_radiation_wavelength / pdbx_data_processing_status ...diffrn_radiation_wavelength / pdbx_data_processing_status / pdbx_validate_close_contact / struct_conn / struct_conn_type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Toxin HigB-2
B: Nanobody 2
C: Toxin HigB-2
D: Nanobody 2
E: Toxin HigB-2
F: Nanobody 2
G: Toxin HigB-2
H: Nanobody 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,10924
Polymers108,4108
Non-polymers1,70016
Water2,342130
1
A: Toxin HigB-2
B: Nanobody 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5087
Polymers27,1022
Non-polymers4065
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-21 kcal/mol
Surface area11370 Å2
MethodPISA
2
C: Toxin HigB-2
D: Nanobody 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7978
Polymers27,1022
Non-polymers6946
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-20 kcal/mol
Surface area12610 Å2
MethodPISA
3
E: Toxin HigB-2
F: Nanobody 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5315
Polymers27,1022
Non-polymers4283
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-22 kcal/mol
Surface area12520 Å2
MethodPISA
4
G: Toxin HigB-2
H: Nanobody 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2744
Polymers27,1022
Non-polymers1712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-12 kcal/mol
Surface area11340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.000, 109.280, 117.480
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain C
31chain E
41chain G
12chain B
22chain D
32chain F
42chain H

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA0 - 109
211chain CC0 - 110
311chain EE0 - 110
411chain GG0 - 110
112chain BB2 - 122
212chain DD2 - 128
312chain FF2 - 128
412chain HH2 - 123

NCS ensembles :
ID
1
2

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Components

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Protein / Antibody , 2 types, 8 molecules ACEGBDFH

#1: Protein
Toxin HigB-2


Mass: 13164.109 Da / Num. of mol.: 4
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 2


Mass: 13938.359 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)

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Non-polymers , 6 types, 146 molecules

#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#7: Chemical ChemComp-PDO / 1,3-PROPANDIOL


Mass: 76.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 45.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M Lithiumsulphate; 0.1M Tris pH8.5; 30% (w/v) PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 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: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.49→49.545 Å / Num. obs: 34841 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 7.24 % / Biso Wilson estimate: 43.89 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.179 / Net I/σ(I): 9.17
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.49-2.641.3511.47196.7
2.64-2.820.8832.361100
2.82-3.050.5144.011100
3.05-3.340.36.65199.9
3.34-3.730.16810.81100
3.73-4.30.10316.12199.9
4.3-5.260.07220.361100
5.26-7.40.07818.991100
7.4-49.5450.05224.63198.8

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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: 2.49→46.476 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.81
RfactorNum. reflection% reflection
Rfree0.2476 1737 5 %
Rwork0.2013 --
obs0.2036 34755 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 165.56 Å2 / Biso mean: 50.0384 Å2 / Biso min: 19.38 Å2
Refinement stepCycle: final / Resolution: 2.49→46.476 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7246 0 157 130 7533
Biso mean--80.47 38.77 -
Num. residues----922
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067494
X-RAY DIFFRACTIONf_angle_d1.03110093
X-RAY DIFFRACTIONf_chiral_restr0.0421051
X-RAY DIFFRACTIONf_plane_restr0.0041301
X-RAY DIFFRACTIONf_dihedral_angle_d14.5642707
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2013X-RAY DIFFRACTION12.777TORSIONAL
12C2013X-RAY DIFFRACTION12.777TORSIONAL
13E2013X-RAY DIFFRACTION12.777TORSIONAL
14G2013X-RAY DIFFRACTION12.777TORSIONAL
21B2250X-RAY DIFFRACTION12.777TORSIONAL
22D2250X-RAY DIFFRACTION12.777TORSIONAL
23F2250X-RAY DIFFRACTION12.777TORSIONAL
24H2250X-RAY DIFFRACTION12.777TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4897-2.5630.38471340.33332554268894
2.563-2.64570.35421440.307727282872100
2.6457-2.74020.33931440.291927312875100
2.7402-2.84990.29261430.261827302873100
2.8499-2.97960.30891440.260427252869100
2.9796-3.13670.2751440.250327352879100
3.1367-3.33310.30731460.234327752921100
3.3331-3.59040.27421450.198827492894100
3.5904-3.95150.22891440.171527562900100
3.9515-4.52290.17621470.145227982945100
4.5229-5.69680.1911480.141428112959100
5.6968-46.48440.21771540.18472926308099
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)
11.98610.11471.66755.32292.50665.60990.02140.17160.0592-0.2915-0.08790.087-0.3655-0.29020.04610.23810.020.06150.31110.03780.289299.21614.401526.7033
24.38-0.35641.92592.49671.85555.7266-0.0232-0.40130.19190.24790.1445-0.204-0.2025-0.0793-0.10810.2776-0.0192-0.00440.2279-0.04530.3134112.717720.297948.4138
34.17990.8046-1.74725.3022-1.80582.58690.0060.1663-0.3844-0.31020.00120.04950.26350.14880.00640.24110.0233-0.05630.3691-0.12690.3317126.7653-4.471929.2306
42.9661-0.2871-1.92820.72620.25595.60750.031-0.519-0.52280.09270.082-0.02780.5330.0998-0.11260.3068-0.0035-0.0390.32110.09590.4501111.0401-8.439551.6104
53.75150.4598-2.14395.7618-2.86533.58770.12080.0928-0.1465-0.1599-0.18350.05540.09420.13460.0630.27030.036-0.05920.3663-0.04260.2296126.8093-60.524255.5563
62.5667-0.3225-1.16881.36860.33834.8228-0.0144-0.29760.01410.1390.04620.03810.1047-0.1274-0.05240.1994-0.0102-0.03470.3023-0.01930.2847110.9799-64.156478.0005
72.52450.64562.1073.79622.58735.2044-0.042-0.00970.2131-0.3370.03230.2371-0.9959-0.4110.02250.5730.2110.09560.51940.08350.384199.6495-40.29353.3744
83.63840.20050.59083.54081.35663.54440.371-0.30150.34190.0918-0.1093-0.1972-1.0307-0.0696-0.23910.6647-0.02250.11260.3179-0.05870.4688113.1319-35.689375.7443
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 110 )A0 - 110
2X-RAY DIFFRACTION2chain 'B' and (resid 2 through 122 )B2 - 122
3X-RAY DIFFRACTION3chain 'C' and (resid 0 through 110 )C0 - 110
4X-RAY DIFFRACTION4chain 'D' and (resid 2 through 128 )D2 - 128
5X-RAY DIFFRACTION5chain 'E' and (resid 0 through 110 )E0 - 110
6X-RAY DIFFRACTION6chain 'F' and (resid 2 through 128 )F2 - 128
7X-RAY DIFFRACTION7chain 'G' and (resid 0 through 110 )G0 - 110
8X-RAY DIFFRACTION8chain 'H' and (resid 2 through 124 )H2 - 124

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