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- PDB-8a0x: Crystal structure of the HigB2-HigA2 tetramer in complex with ope... -

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Basic information

Entry
Database: PDB / ID: 8a0x
TitleCrystal structure of the HigB2-HigA2 tetramer in complex with operator DNA
Components
  • Antitoxin HigA-2
  • DNA (30-MER)
  • DNA (31-MER)
  • Toxin HigB-2
KeywordsDNA BINDING PROTEIN / antitoxin / HigA2 / repressor / toxin-antitoxin module / HigB2 / Vibrio cholerae
Function / homology
Function and homology information


Toxin HigB-2 / RelE toxin of RelE / RelB toxin-antitoxin system / Antitoxin 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
Similarity search - Domain/homology
DNA / DNA (> 10) / Antitoxin HigA-2 / Toxin HigB-2
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.296 Å
AuthorsHadzi, S. / Loris, R.
Funding support Slovenia, Belgium, 2items
OrganizationGrant numberCountry
Slovenian Research AgencyP1-0201 Slovenia
Research Foundation - Flanders (FWO)G003320N Belgium
CitationJournal: To Be Published
Title: Fuzzy DNA recognition by a prokaryotic transcription factor
Authors: Hadzi, S. / Loris, R.
History
DepositionMay 30, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 3, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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 HigA-2
B: Antitoxin HigA-2
C: Toxin HigB-2
D: Toxin HigB-2
E: DNA (30-MER)
F: DNA (31-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,09116
Polymers68,8486
Non-polymers24310
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.620, 113.620, 121.050
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain C
21(chain D and (resid 2 through 38 or (resid 39...
12(chain A and (resid 2 through 8 or (resid 9...
22chain B

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LYSLYSGLNGLNchain CCC2 - 1095 - 112
211LYSLYSGLYGLY(chain D and (resid 2 through 38 or (resid 39...DD2 - 385 - 41
221ASPASPASPASP(chain D and (resid 2 through 38 or (resid 39...DD3942
231HISHISGLNGLN(chain D and (resid 2 through 38 or (resid 39...DD0 - 1093 - 112
241HISHISGLNGLN(chain D and (resid 2 through 38 or (resid 39...DD0 - 1093 - 112
251HISHISGLNGLN(chain D and (resid 2 through 38 or (resid 39...DD0 - 1093 - 112
261HISHISGLNGLN(chain D and (resid 2 through 38 or (resid 39...DD0 - 1093 - 112
112SERSERALAALA(chain A and (resid 2 through 8 or (resid 9...AA2 - 81 - 7
122GLUGLUGLUGLU(chain A and (resid 2 through 8 or (resid 9...AA98
132SERSERLEULEU(chain A and (resid 2 through 8 or (resid 9...AA2 - 1041 - 103
142SERSERLEULEU(chain A and (resid 2 through 8 or (resid 9...AA2 - 1041 - 103
152SERSERLEULEU(chain A and (resid 2 through 8 or (resid 9...AA2 - 1041 - 103
162SERSERLEULEU(chain A and (resid 2 through 8 or (resid 9...AA2 - 1041 - 103
212SERSERLEULEUchain BBB2 - 1041 - 103

NCS ensembles :
ID
1
2

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Components

#1: Protein Antitoxin HigA-2


Mass: 11581.993 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: higA-2, VC_A0469
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9KMA5
#2: Protein Toxin HigB-2


Mass: 13308.240 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: higB-2, VC_A0468
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9KMA6
#3: DNA chain DNA (30-MER)


Mass: 9431.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Vibrio cholerae (bacteria)
#4: DNA chain DNA (31-MER)


Mass: 9636.210 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Vibrio cholerae (bacteria)
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestN

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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: 2.84 Å3/Da / Density % sol: 56.65 % / Description: rectangular
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M potassium iodide, 0.1 M MES pH 6.5, 25% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 3.29→48.342 Å / Num. obs: 12408 / % possible obs: 99.3 % / Redundancy: 7 % / Rrim(I) all: 0.187 / Net I/σ(I): 12.3
Reflection shellResolution: 3.3→3.49 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 2 / Num. unique obs: 1921 / Rrim(I) all: 1.23 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JAA

5jaa


Resolution: 3.296→48.342 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 28.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2674 620 5 %
Rwork0.238 11775 -
obs0.2395 12395 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 232.96 Å2 / Biso mean: 97.1163 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 3.296→48.342 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3282 1247 10 0 4539
Biso mean--30 --
Num. residues----485
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064794
X-RAY DIFFRACTIONf_angle_d1.0096740
X-RAY DIFFRACTIONf_chiral_restr0.051751
X-RAY DIFFRACTIONf_plane_restr0.006658
X-RAY DIFFRACTIONf_dihedral_angle_d22.9642635
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11C942X-RAY DIFFRACTION14.025TORSIONAL
12D942X-RAY DIFFRACTION14.025TORSIONAL
21A936X-RAY DIFFRACTION14.025TORSIONAL
22B936X-RAY DIFFRACTION14.025TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.296-3.62750.38351510.3476285799
3.6275-4.15220.29921530.26832913100
4.1522-5.23030.25291550.22682947100
5.2303-48.3420.22941610.2019305898
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)
11.7837-1.2875-0.40476.18641.05312.3750.02820.137-0.08730.2578-0.0656-0.0773-0.30560.31390.10060.30760.0039-0.1030.4880.02630.43822.85350.8006-0.0621
23.68031.40571.35991.76950.03733.9626-0.22120.26640.0292-0.07350.2384-0.0373-0.5480.64850.01740.4165-0.03520.08570.5326-0.03670.6075.713858.8071-11.8397
31.1655-0.5419-0.741.0105-1.26254.0751-0.254-0.07640.42940.50780.3171-0.409-0.66990.70370.061.2355-0.6623-0.10131.30840.09910.983323.416477.1395-4.843
46.7126-0.422-0.66297.404-0.69198.02790.29280.79820.1481-0.4117-0.43390.42860.4893-0.07230.15040.46250.1733-0.03370.5366-0.04680.69783.473425.5546-6.7239
53.08880.18381.83142.1823.4525.6841-0.0562-0.3704-0.06320.0108-0.31240.1949-0.1638-0.79680.23340.61890.07740.09790.65090.10680.5205-14.533861.8374-5.7257
64.08791.18382.14562.07353.20084.6212-0.0198-0.1231-0.36480.0148-0.1753-0.1017-0.1475-0.66450.16420.72060.11070.07970.70350.14080.6516-15.530558.0652-7.2197
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 2 through 104)A2 - 104
2X-RAY DIFFRACTION2(chain 'B' and resid 2 through 104)B2 - 104
3X-RAY DIFFRACTION3(chain 'C' and resid 2 through 109)C2 - 109
4X-RAY DIFFRACTION4(chain 'D' and resid 0 through 109)D0 - 109
5X-RAY DIFFRACTION5(chain 'E' and resid 3 through 33)E3 - 33
6X-RAY DIFFRACTION6(chain 'F' and resid 4 through 34)F4 - 34

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