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- PDB-8ke8: Crystal structure of TetR-type transcriptional factor NalC from P... -

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Basic information

Entry
Database: PDB / ID: 8ke8
TitleCrystal structure of TetR-type transcriptional factor NalC from P. aeruginosa
ComponentsNalC
KeywordsDNA BINDING PROTEIN / NalC / TetR-type transcriptional factor / Multi-drug efflux system
Function / homology
Function and homology information


negative regulation of transmembrane transport / transcription cis-regulatory region binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription
Similarity search - Function
Transcriptional regulator TetR, C-terminal, Proteobacteria type / AefR-like transcriptional repressor, C-terminal domain / : / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily
Similarity search - Domain/homology
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsLee, J.Y. / Jeong, K.H. / Ko, J.H. / Son, S.B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2023
Title: Structural insights into the transcriptional regulator NalC, a key component of the MexAB-OprM efflux pump system, from Pseudomonas aeruginosa.
Authors: Jeong, K.H. / Ko, J.H. / Son, S.B. / Lee, J.Y.
History
DepositionAug 11, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NalC
B: NalC


Theoretical massNumber of molelcules
Total (without water)47,1182
Polymers47,1182
Non-polymers00
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-32 kcal/mol
Surface area17360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.517, 57.517, 224.345
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein NalC


Mass: 23558.914 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: nalC / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q9HXS0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 2.44 Å3/Da / Density % sol: 49.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.25
Details: 0.2 M Ammonium chloride, 0.1 M MES pH 6.25, 1.0 M Potassium sodium tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1.00003 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 26116 / % possible obs: 99.8 % / Redundancy: 11.6 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 34.52
Reflection shellResolution: 2.05→2.09 Å / Rmerge(I) obs: 0.361 / Num. unique obs: 1257

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Processing

Software
NameVersionClassification
PHENIX(1.19.1_4122: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 2.05→19.67 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 29.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2492 2002 7.7 %
Rwork0.2099 --
obs0.2129 26011 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→19.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2969 0 0 133 3102
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023026
X-RAY DIFFRACTIONf_angle_d0.5314097
X-RAY DIFFRACTIONf_dihedral_angle_d3.798424
X-RAY DIFFRACTIONf_chiral_restr0.033478
X-RAY DIFFRACTIONf_plane_restr0.004524
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.10.3531390.26691640X-RAY DIFFRACTION99
2.1-2.160.31651470.25391741X-RAY DIFFRACTION100
2.16-2.220.28681440.25341715X-RAY DIFFRACTION100
2.22-2.30.28791490.23831717X-RAY DIFFRACTION100
2.3-2.380.29681430.24391719X-RAY DIFFRACTION100
2.38-2.470.27191400.23541691X-RAY DIFFRACTION100
2.47-2.590.30531490.23951727X-RAY DIFFRACTION100
2.59-2.720.28661350.24541724X-RAY DIFFRACTION100
2.72-2.890.28441410.23811728X-RAY DIFFRACTION100
2.89-3.110.27221430.24761712X-RAY DIFFRACTION100
3.11-3.430.28591460.21241714X-RAY DIFFRACTION100
3.43-3.920.23991450.18831718X-RAY DIFFRACTION100
3.92-4.920.18161440.16851733X-RAY DIFFRACTION100
4.93-19.670.20991370.18911730X-RAY DIFFRACTION99

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