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- PDB-3ga8: Structure of the N-terminal domain of the E. coli protein MqsA (Y... -

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Basic information

Entry
Database: PDB / ID: 3ga8
TitleStructure of the N-terminal domain of the E. coli protein MqsA (YgiT/b3021)
ComponentsHTH-type transcriptional regulator MqsA (YgiT/B3021)
KeywordsDNA BINDING PROTEIN / helix-turn-helix / Zn-binding protein / DNA-binding / Transcription / Transcription regulation
Function / homology
Function and homology information


toxin-antitoxin complex / single-species biofilm formation / sequence-specific DNA binding / regulation of DNA-templated transcription / protein homodimerization activity / metal ion binding
Similarity search - Function
Ubiquitin-like (UB roll) - #860 / Antitoxin MqsA / Zinc finger, MqsA-type / Antitoxin MqsA/HigA-2 / : / Antitoxin component of bacterial toxin-antitoxin system, MqsA / 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) - #860 / Antitoxin MqsA / Zinc finger, MqsA-type / Antitoxin MqsA/HigA-2 / : / Antitoxin component of bacterial toxin-antitoxin system, MqsA / 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 / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsBrown, 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
DepositionFeb 16, 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HTH-type transcriptional regulator MqsA (YgiT/B3021)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1343
Polymers8,7141
Non-polymers4202
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)30.841, 52.106, 53.767
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HTH-type transcriptional regulator MqsA (YgiT/B3021)


Mass: 8714.171 Da / Num. of mol.: 1 / Fragment: 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: RP1B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 RIL / References: UniProt: Q46864
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.48 Å3/Da / Density % sol: 50.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.1
Details: 30% PEG 4000, 0.1M Tris, 0.2M sodium selenate, pH 8.1, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X6A10.9787
SYNCHROTRONNSLS X6A20.9321
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 2701CCDDec 4, 2008Toroidal focusing mirror
ADSC QUANTUM 2702CCDDec 4, 2008Toroidal focusing mirror
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si (111) channel cut monochromatorSADMx-ray1
2Si (111) channel cut monochromatorSADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97871
20.93211
ReflectionResolution: 1.7→50 Å / Num. all: 10054 / Num. obs: 9796 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 15.9 Å2 / Rsym value: 0.057 / Net I/σ(I): 21.1
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 6.62 / Num. unique all: 484 / Rsym value: 0.262 / % possible all: 96.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXSphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.7→37.42 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.589 / SU ML: 0.048 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.089 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18559 467 4.8 %RANDOM
Rwork0.1649 ---
all0.16591 9308 --
obs0.16591 9308 97.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.698 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20 Å2
2---0.2 Å20 Å2
3---0.29 Å2
Refinement stepCycle: LAST / Resolution: 1.7→37.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms511 0 11 97 619
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.022559
X-RAY DIFFRACTIONr_bond_other_d0.0010.02392
X-RAY DIFFRACTIONr_angle_refined_deg1.2831.965757
X-RAY DIFFRACTIONr_angle_other_deg0.8263.004948
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.111580
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.49823.63622
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.26315101
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.827153
X-RAY DIFFRACTIONr_chiral_restr0.0810.284
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02627
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02112
X-RAY DIFFRACTIONr_nbd_refined0.2140.292
X-RAY DIFFRACTIONr_nbd_other0.1920.2382
X-RAY DIFFRACTIONr_nbtor_refined0.1680.2277
X-RAY DIFFRACTIONr_nbtor_other0.0840.2297
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.258
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2380.23
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2780.212
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2120.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7993376
X-RAY DIFFRACTIONr_mcbond_other0.4433143
X-RAY DIFFRACTIONr_mcangle_it2.5185574
X-RAY DIFFRACTIONr_scbond_it3.7618219
X-RAY DIFFRACTIONr_scangle_it5.43211176
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.743 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 30 -
Rwork0.159 661 -
obs--97.46 %
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)
17.8126-3.9548-1.48122.33311.11983.5477-0.4135-0.59290.08110.22260.3761-0.05390.33720.35890.0375-0.02040.00760.00510.0025-0.0262-0.02125.2172-7.920913.3884
20.47820.46960.64062.23871.08236.0813-0.03250.02790.0232-0.12220.1279-0.1729-0.29770.1717-0.0954-0.0175-0.0077-0.0012-0.0138-0.0004-0.0292-9.437-3.6107-3.9127
30.7066-0.3788-0.49670.71590.12961.2568-0.1694-0.11230.1314-0.1060.0897-0.1148-0.0641-0.23880.07970.0081-0.0059-0.0066-0.0459-0.02-0.0113-5.251-2.62716.8939
43.295-0.39711.56690.0564-0.18710.7455-0.03030.00720.0431-0.00740.008-0.0090.0134-0.08580.0223-0.01150.00110.0167-0.0045-0.006-0.0094-7.7781-10.65898.819
54.45291.42054.91440.83242.8049.4539-0.02490.05950.149-0.3658-0.01360.1654-0.2008-0.16620.0385-0.0107-0.0098-0.0147-0.04790.005-0.0055-16.815-7.9861-5.6817
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 15
2X-RAY DIFFRACTION2A16 - 25
3X-RAY DIFFRACTION3A26 - 39
4X-RAY DIFFRACTION4A40 - 56
5X-RAY DIFFRACTION5A57 - 67

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