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- PDB-5j9i: Crystal structure of the HigA2 antitoxin C-terminal domain -

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Basic information

Entry
Database: PDB / ID: 5j9i
TitleCrystal structure of the HigA2 antitoxin C-terminal domain
ComponentsAntitoxin igA-2
KeywordsANTITOXIN / toxin-antitoxin system
Function / homologyAntitoxin MqsA/HigA-2 / Antitoxin component of bacterial toxin-antitoxin system, MqsA / Cro/C1-type helix-turn-helix domain / Lambda repressor-like, DNA-binding domain superfamily / DNA binding / Antitoxin HigA-2
Function and homology information
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.797 Å
AuthorsHadzi, S. / Loris, R.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Fonds voor Wetenschappelijk Onderzoek VlaanderenG.0135.15N Belgium
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 10, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1May 17, 2017Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Antitoxin igA-2
B: Antitoxin igA-2
C: Antitoxin igA-2
D: Antitoxin igA-2
E: Antitoxin igA-2
F: Antitoxin igA-2
G: Antitoxin igA-2
H: Antitoxin igA-2


Theoretical massNumber of molelcules
Total (without water)93,7068
Polymers93,7068
Non-polymers00
Water4,234235
1
A: Antitoxin igA-2
B: Antitoxin igA-2


Theoretical massNumber of molelcules
Total (without water)23,4262
Polymers23,4262
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-12 kcal/mol
Surface area7110 Å2
MethodPISA
2
C: Antitoxin igA-2
D: Antitoxin igA-2


Theoretical massNumber of molelcules
Total (without water)23,4262
Polymers23,4262
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-12 kcal/mol
Surface area7330 Å2
MethodPISA
3
E: Antitoxin igA-2
F: Antitoxin igA-2


Theoretical massNumber of molelcules
Total (without water)23,4262
Polymers23,4262
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-12 kcal/mol
Surface area6880 Å2
MethodPISA
4
G: Antitoxin igA-2
H: Antitoxin igA-2


Theoretical massNumber of molelcules
Total (without water)23,4262
Polymers23,4262
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-13 kcal/mol
Surface area7040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.360, 61.160, 73.850
Angle α, β, γ (deg.)90.000, 106.690, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-237-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D
51chain E
61chain F
71chain G
81chain H

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: LEU / End label comp-ID: LEU

Dom-IDBeg auth comp-IDBeg label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1LEULEUchain AAA38 - 10438 - 104
2GLUGLUchain BBB37 - 10437 - 104
3GLYGLYchain CCC36 - 10436 - 104
4GLUGLUchain DDD37 - 10437 - 104
5ASNASNchain EEE39 - 10439 - 104
6GLUGLUchain FFF37 - 10437 - 104
7ILEILEchain GGG40 - 10440 - 104
8GLUGLUchain HHH37 - 10437 - 104

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Components

#1: Protein
Antitoxin igA-2


Mass: 11713.190 Da / Num. of mol.: 8 / Fragment: C-terminal domainn
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: higA-2, VC_A0469 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KMA5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / 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 Å3/Da / Density % sol: 38.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM Tris HCl pH 8.5, 200 mM calcium chloride, 20% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 5, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 1.797→45.854 Å / Num. obs: 44925 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Redundancy: 3.99 % / Biso Wilson estimate: 26.65 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.053 / Net I/σ(I): 12.88
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.8-1.910.4092.27191.4
1.91-2.040.2434.96199.1
2.04-2.20.1498.35198.9
2.2-2.410.1111.6198.6
2.41-2.690.08214.91198.4
2.69-3.110.05419.41198.4
3.11-3.80.04324.63198.7
3.8-5.360.03828.34199.3
5.36-45.8540.03627.25197.9

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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: 1.797→38.507 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 30.53
RfactorNum. reflection% reflection
Rfree0.2357 2242 5 %
Rwork0.194 --
obs0.1961 44840 97.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 112.4 Å2 / Biso mean: 37.2654 Å2 / Biso min: 13.76 Å2
Refinement stepCycle: final / Resolution: 1.797→38.507 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4255 0 0 235 4490
Biso mean---37.71 -
Num. residues----539
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134346
X-RAY DIFFRACTIONf_angle_d1.3625895
X-RAY DIFFRACTIONf_chiral_restr0.058689
X-RAY DIFFRACTIONf_plane_restr0.007770
X-RAY DIFFRACTIONf_dihedral_angle_d12.8321623
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3273X-RAY DIFFRACTION16.278TORSIONAL
12B3273X-RAY DIFFRACTION16.278TORSIONAL
13C3273X-RAY DIFFRACTION16.278TORSIONAL
14D3273X-RAY DIFFRACTION16.278TORSIONAL
15E3273X-RAY DIFFRACTION16.278TORSIONAL
16F3273X-RAY DIFFRACTION16.278TORSIONAL
17G3273X-RAY DIFFRACTION16.278TORSIONAL
18H3273X-RAY DIFFRACTION16.278TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7971-1.83620.33881160.29532206232282
1.8362-1.87890.32981380.27622626276497
1.8789-1.92590.29731430.25162706284999
1.9259-1.9780.28691410.2342682282399
1.978-2.03620.25251410.22362678281999
2.0362-2.10190.27081410.21272687282899
2.1019-2.1770.26861430.20052715285899
2.177-2.26420.27561400.19542648278899
2.2642-2.36720.281400.1952677281799
2.3672-2.4920.25141410.19642678281998
2.492-2.64810.27261420.19892707284998
2.6481-2.85250.20741420.19872683282598
2.8525-3.13940.26311420.20192700284299
3.1394-3.59340.23051430.17892722286599
3.5934-4.52620.16931440.15732724286899
4.5262-38.5160.21621450.19112759290498
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)
10.7759-0.5287-0.48220.52430.29650.63540.096-0.19220.1428-0.0246-0.0131-0.1742-0.09790.13730.00020.1976-0.03050.00760.2192-0.02990.17415.8343-10.950421.2888
20.44090.0934-0.42660.88130.28481.6063-0.04670.1425-0.042-0.2469-0.0276-0.24470.05260.0417-0.00010.25720.01430.02410.20060.01330.272714.0564-22.91228.7545
30.99330.218-0.45370.8024-0.67740.65580.14110.09340.1084-0.0009-0.03160.1169-0.1666-0.1035-0.00010.21270.01180.03020.18350.00220.1623-16.1777-10.755114.7101
40.8378-0.3569-0.9710.55180.18141.2471-0.0896-0.1247-0.21080.0601-0.05550.07290.03920.0510.00070.2241-0.00510.02490.2020.02610.2448-23.668-22.853627.4315
50.47-0.30830.52521.071-0.41290.58130.10940.0515-0.24050.1241-0.09190.2090.10810.11610.00010.2296-0.00780.00870.1853-0.01040.2423-15.7659-50.929721.9956
60.46010.28120.61060.7653-0.06821.1375-0.06080.21760.0344-0.2011-0.09450.22980.0340.0199-0.00090.2471-0.01050.00210.26640.00710.2874-23.998-39.84138.4364
70.46540.14830.18771.30760.36750.5531-0.01140.2951-0.2539-0.25320.0182-0.28120.1732-0.14160.00040.2547-0.02360.02160.2944-0.01470.24846.0583-50.704514.1311
80.53110.0630.12270.8616-0.27250.964-0.0977-0.12490.16750.10940.0654-0.0043-0.1004-0.16160.00020.2356-0.001-0.01230.24110.00970.241814.0656-39.849727.8671
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 38 through 104)A38 - 104
2X-RAY DIFFRACTION2chain 'B' and (resid 37 through 104 )B37 - 104
3X-RAY DIFFRACTION3chain 'C' and (resid 36 through 104 )C36 - 104
4X-RAY DIFFRACTION4chain 'D' and (resid 37 through 104 )D37 - 104
5X-RAY DIFFRACTION5chain 'E' and (resid 39 through 104)E39 - 104
6X-RAY DIFFRACTION6chain 'F' and (resid 37 through 104)F37 - 104
7X-RAY DIFFRACTION7chain 'G' and (resid 40 through 104)G40 - 104
8X-RAY DIFFRACTION8chain 'H' and (resid 37 through 104)H37 - 104

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