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- PDB-3hi2: Structure of the N-terminal domain of the E. coli antitoxin MqsA ... -

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Basic information

Entry
Database: PDB / ID: 3hi2
TitleStructure of the N-terminal domain of the E. coli antitoxin MqsA (YgiT/b3021) in complex with the E. coli toxin MqsR (YgiU/b3022)
Components
  • HTH-type transcriptional regulator mqsA(ygiT)
  • Motility quorum-sensing regulator mqsR
KeywordsDNA BINDING PROTEIN/TOXIN / Toxin-Antitoxin system / Zn-binding protein / mqsR / mqsA / ygiU / ygiT / B3022 / B3021 / stress response / quorum sensing / DNA BINDING PROTEIN-TOXIN complex
Function / homology
Function and homology information


toxin-antitoxin complex / quorum sensing / single-species biofilm formation / regulation of cell motility / RNA endonuclease activity / regulation of mRNA stability / negative regulation of translation / sequence-specific DNA binding / Hydrolases; Acting on ester bonds / negative regulation of DNA-templated transcription ...toxin-antitoxin complex / quorum sensing / single-species biofilm formation / regulation of cell motility / RNA endonuclease activity / regulation of mRNA stability / negative regulation of translation / sequence-specific DNA binding / Hydrolases; Acting on ester bonds / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / protein homodimerization activity / metal ion binding
Similarity search - Function
YaeB-like fold - #40 / mRNA interferase toxin MqsR / Toxin MqsR superfamily / Motility quorum-sensing regulator, toxin of MqsA / Ubiquitin-like (UB roll) - #860 / Antitoxin MqsA / Zinc finger, MqsA-type / Antitoxin MqsA/HigA-2 / Antitoxin component of bacterial toxin-antitoxin system, MqsA / YaeB-like fold ...YaeB-like fold - #40 / mRNA interferase toxin MqsR / Toxin MqsR superfamily / Motility quorum-sensing regulator, toxin of MqsA / Ubiquitin-like (UB roll) - #860 / Antitoxin MqsA / Zinc finger, MqsA-type / Antitoxin MqsA/HigA-2 / Antitoxin component of bacterial toxin-antitoxin system, MqsA / YaeB-like fold / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / Lambda repressor-like, DNA-binding domain superfamily / Ubiquitin-like (UB roll) / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Antitoxin MqsA / mRNA interferase toxin MqsR
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsGrigoriu, S. / Brown, B.L. / Arruda, J.M. / Peti, W. / Page, R.
CitationJournal: Plos Pathog. / Year: 2009
Title: Three dimensional structure of the MqsR:MqsA complex: a novel TA pair comprised of a toxin homologous to RelE and an antitoxin with unique properties.
Authors: Brown, B.L. / Grigoriu, S. / Kim, Y. / Arruda, J.M. / Davenport, A. / Wood, T.K. / Peti, W. / Page, R.
History
DepositionMay 18, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HTH-type transcriptional regulator mqsA(ygiT)
B: Motility quorum-sensing regulator mqsR
C: HTH-type transcriptional regulator mqsA(ygiT)
D: Motility quorum-sensing regulator mqsR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4138
Polymers40,0984
Non-polymers3154
Water3,513195
1
A: HTH-type transcriptional regulator mqsA(ygiT)
B: Motility quorum-sensing regulator mqsR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2995
Polymers20,0492
Non-polymers2503
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-8 kcal/mol
Surface area9420 Å2
MethodPISA
2
C: HTH-type transcriptional regulator mqsA(ygiT)
D: Motility quorum-sensing regulator mqsR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1153
Polymers20,0492
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-8 kcal/mol
Surface area8360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.234, 63.234, 194.886
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Refine code: 4

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
211METMETTYRTYRCC1 - 201 - 20
121THRTHRASNASNAA27 - 6527 - 65
221THRTHRASNASNCC27 - 6527 - 65
112GLUGLUTHRTHRBB2 - 605 - 63
212GLUGLUTHRTHRDD2 - 605 - 63
122HISHISVALVALBB64 - 8667 - 89
222HISHISVALVALDD64 - 8667 - 89
132LEULEUPHEPHEBB91 - 9594 - 98
232LEULEUPHEPHEDD91 - 9594 - 98

NCS ensembles :
ID
1
2

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Components

#1: Protein HTH-type transcriptional regulator mqsA(ygiT)


Mass: 8518.972 Da / Num. of mol.: 2 / Fragment: MqsA N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: Escherichia coli str. K12 / Gene: b3021, JW2989, ygiT / Plasmid: pCA21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: Q46864
#2: Protein Motility quorum-sensing regulator mqsR


Mass: 11530.237 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: Escherichia coli str. K12 / Gene: b3022, JW2990, mqsR, ygiU / Plasmid: pET-28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: Q46865
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 2.43 Å3/Da / Density % sol: 49.37 %
Crystal growTemperature: 277 K / pH: 5.6
Details: 0.1M Bis Tris, 25% PEG 3350, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
1,2,31
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONNSLS X6A11
SYNCHROTRONNSLS X6A21.2815
SYNCHROTRONNSLS X6A31.283
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 2701CCDApr 10, 2009TOROIDAL FOCUSING MIRROR
ADSC QUANTUM 2702CCDApr 10, 2009TOROIDAL FOCUSING MIRROR
ADSC QUANTUM 2703CCDApr 10, 2009TOROIDAL FOCUSING MIRROR
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SI (111) CHANNEL CUT MONOCHROMATORMADMx-ray1
2SI (111) CHANNEL CUT MONOCHROMATORMADMx-ray1
3SI (111) CHANNEL CUT MONOCHROMATORMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.28151
31.2831
ReflectionResolution: 2→50 Å / Num. obs: 26665 / % possible obs: 95.8 % / Redundancy: 12.5 % / Biso Wilson estimate: 27.9 Å2 / Rsym value: 0.058 / Net I/σ(I): 35.99
Reflection shellResolution: 2→2.03 Å / Redundancy: 11.6 % / Mean I/σ(I) obs: 8.56 / Rsym value: 0.365 / % possible all: 98

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2→40.64 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.917 / SU B: 8.142 / SU ML: 0.112 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.183 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1337 5 %RANDOM
Rwork0.205 ---
obs0.207 25311 96 %-
all-25311 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.98 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å20 Å2
2---0.15 Å20 Å2
3---0.29 Å2
Refinement stepCycle: LAST / Resolution: 2→40.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2468 0 14 195 2677
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222551
X-RAY DIFFRACTIONr_bond_other_d0.0010.021702
X-RAY DIFFRACTIONr_angle_refined_deg1.3381.9523447
X-RAY DIFFRACTIONr_angle_other_deg0.88434174
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7965321
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.35523.925107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.17115459
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.451514
X-RAY DIFFRACTIONr_chiral_restr0.0820.2404
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022777
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02499
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.60431583
X-RAY DIFFRACTIONr_mcbond_other0.6113646
X-RAY DIFFRACTIONr_mcangle_it2.64652572
X-RAY DIFFRACTIONr_scbond_it4.3888968
X-RAY DIFFRACTIONr_scangle_it6.36611870
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A709MEDIUM POSITIONAL0.330.5
1A709MEDIUM THERMAL1.1932
2B1088MEDIUM POSITIONAL0.5130.5
2B1088MEDIUM THERMAL1.0382
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 99 -
Rwork0.237 1864 -
obs--97.61 %
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)
11.0925-0.30190.07281.04230.72694.7085-0.0636-0.032-0.1150.14590.0776-0.06450.1830.1365-0.0140.03380.00620.01040.02460.00420.0614-0.1743-21.8311-5.7952
22.0346-1.3532-0.73181.82180.89251.92010.11310.34640.0331-0.0556-0.1434-0.1667-0.2134-0.05170.03030.03460.0017-0.01630.10550.00070.032-4.2087-12.0346-23.0474
30.83562.0166-0.54739.8836-1.51230.50920.4885-0.23580.1830.7175-0.19270.3874-0.383-0.015-0.29580.3772-0.06650.19010.34020.04040.3843-21.3112-43.4456-8.4609
41.71261.4525-0.38086.87861.70144.5686-0.07420.1924-0.2234-0.18230.20540.56330.2501-0.029-0.13120.1799-0.0063-0.02770.14180.00910.2975-16.5164-40.943-26.9381
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 70
2X-RAY DIFFRACTION2B1 - 97
3X-RAY DIFFRACTION3C1 - 65
4X-RAY DIFFRACTION4D2 - 95

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