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- PDB-6l33: Crystal structure of the regulatory domain of MexT, a transcripti... -

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Basic information

Entry
Database: PDB / ID: 6l33
TitleCrystal structure of the regulatory domain of MexT, a transcriptional activator in Pseudomonas aeruginosa
ComponentsMexT protein
KeywordsTRANSCRIPTION / LysR-type transcriptional regulator / antibiotic resistance / regulatory domain
Function / homology
Function and homology information


negative regulation of secondary metabolite biosynthetic process / DNA-binding transcription activator activity / negative regulation of protein secretion / protein-DNA complex / negative regulation of proteolysis / transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription
Similarity search - Function
LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
MexT protein / Transcriptional regulator MexT
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsKim, S. / Ha, N.-C.
CitationJournal: Mol.Cells / Year: 2019
Title: Crystal Structure of the Regulatory Domain of MexT, a Transcriptional Activator of the MexEFOprN Efflux Pump inPseudomonas aeruginosa.
Authors: Kim, S. / Kim, S.H. / Ahn, J. / Jo, I. / Lee, Z.W. / Choi, S.H. / Ha, N.
History
DepositionOct 8, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 30, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 15, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MexT protein
B: MexT protein
C: MexT protein
D: MexT protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,2569
Polymers92,7764
Non-polymers4805
Water4,900272
1
A: MexT protein
B: MexT protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6765
Polymers46,3882
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-58 kcal/mol
Surface area17420 Å2
MethodPISA
2
C: MexT protein
D: MexT protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5804
Polymers46,3882
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-54 kcal/mol
Surface area16760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.652, 108.703, 109.230
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
MexT protein


Mass: 23193.961 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: mexT / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O87785, UniProt: Q9I0Z0*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 272 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.12 Å3/Da / Density % sol: 41.92 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop
Details: 0.5 M Ammonium sulfate, 0.1 M lithium sulfate, 1.0 M sodium citrate tribasic dehydrate (pH 5.6), 2 mM EDTA

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 53533 / % possible obs: 97.1 % / Redundancy: 5.6 % / Biso Wilson estimate: 22.18 Å2 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.023 / Rrim(I) all: 0.059 / Net I/σ(I): 23.76
Reflection shellResolution: 2→2.03 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.91 / Num. unique obs: 2444 / CC1/2: 0.633 / Rpim(I) all: 0.19 / Rrim(I) all: 0.4 / % possible all: 93.6

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2→31.84 Å / SU ML: 0.2301 / Cross valid method: FREE R-VALUE / σ(F): 1.5 / Phase error: 22.9803
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.253 1978 3.91 %
Rwork0.2061 48652 -
obs0.2079 50630 94.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.81 Å2
Refinement stepCycle: LAST / Resolution: 2→31.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6060 0 25 272 6357
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00316203
X-RAY DIFFRACTIONf_angle_d0.66558412
X-RAY DIFFRACTIONf_chiral_restr0.0432955
X-RAY DIFFRACTIONf_plane_restr0.00421097
X-RAY DIFFRACTIONf_dihedral_angle_d14.43254158
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.2909960.23052521X-RAY DIFFRACTION69.03
2.05-2.110.28211260.22743109X-RAY DIFFRACTION85.99
2.11-2.170.27011370.22133321X-RAY DIFFRACTION92.36
2.17-2.240.27831380.21253453X-RAY DIFFRACTION94.67
2.24-2.320.26861410.2123486X-RAY DIFFRACTION95.8
2.32-2.410.24381390.21483504X-RAY DIFFRACTION96.22
2.41-2.520.27791460.21263531X-RAY DIFFRACTION97.12
2.52-2.650.26871470.21673580X-RAY DIFFRACTION97.69
2.65-2.820.31961480.21023595X-RAY DIFFRACTION98.66
2.82-3.040.24621460.21453624X-RAY DIFFRACTION98.56
3.04-3.340.24161510.21083651X-RAY DIFFRACTION99.17
3.34-3.820.23621550.19433677X-RAY DIFFRACTION99.4
3.82-4.820.20641500.17493730X-RAY DIFFRACTION99.54
4.82-31.840.2611580.21443870X-RAY DIFFRACTION98.99

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