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- PDB-3bcg: Conformational changes of the AcrR regulator reveal a mechanism o... -

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Basic information

Entry
Database: PDB / ID: 3bcg
TitleConformational changes of the AcrR regulator reveal a mechanism of induction
ComponentsHTH-type transcriptional regulator acrR
KeywordsTRANSCRIPTION regulator / AcrB regulator / DNA-binding / Repressor / Transcription / Transcription regulation / DNA BINDING PROTEIN
Function / homology
Function and homology information


toxic substance binding / sequence-specific DNA binding / transcription cis-regulatory region binding / response to xenobiotic stimulus / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription
Similarity search - Function
Transcription regulator MAATS, C-terminal / MAATS-type transcriptional repressor, C-terminal region / DNA-binding HTH domain, TetR-type, conserved site / TetR-type HTH domain signature. / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. ...Transcription regulator MAATS, C-terminal / MAATS-type transcriptional repressor, C-terminal region / DNA-binding HTH domain, TetR-type, conserved site / TetR-type HTH domain signature. / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HTH-type transcriptional regulator AcrR
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.48 Å
AuthorsGu, R. / Li, M. / Su, C.C. / Long, F. / Yang, F. / McDermott, G. / Yu, E.Y.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2008
Title: Conformational change of the AcrR regulator reveals a possible mechanism of induction.
Authors: Gu, R. / Li, M. / Su, C.C. / Long, F. / Routh, M.D. / Yang, F. / McDermott, G. / Yu, E.W.
History
DepositionNov 12, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HTH-type transcriptional regulator acrR
B: HTH-type transcriptional regulator acrR


Theoretical massNumber of molelcules
Total (without water)49,5952
Polymers49,5952
Non-polymers00
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.660, 46.660, 166.155
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein HTH-type transcriptional regulator acrR / Potential acrAB operon repressor


Mass: 24797.658 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12 / Gene: acrR / Plasmid: PET15B / Species (production host): Escherichia coli / Production host: Escherichia coli K12 (bacteria) / Strain (production host): K-12 / References: UniProt: P0ACS9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.11 Å3/Da / Density % sol: 41.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 35% PEG4000, 0.2M MgCl2, 0.1M Tris , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1 Å
DetectorDetector: CCD / Date: Jul 13, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.48→50 Å / Num. all: 14362 / Num. obs: 14362 / Observed criterion σ(F): 4 / Observed criterion σ(I): 4 / Redundancy: 5.2 % / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 23.2
Reflection shellResolution: 2.48→2.57 Å / Rmerge(I) obs: 0.246 / Mean I/σ(I) obs: 4 / Rsym value: 0.24 / % possible all: 84.5

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Processing

Software
NameClassification
HKL-2000data collection
SnBphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.48→50 Å / σ(F): 4 / σ(I): 4
RfactorNum. reflection
Rfree0.268 -
Rwork0.214 -
all-14362
obs-14362
Refinement stepCycle: LAST / Resolution: 2.48→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3346 0 0 84 3430
Refine LS restraintsType: p_bond_d / Dev ideal: 0.007
LS refinement shellResolution: 2.48→2.57 Å /
Rfactor% reflection
Rfree0.268 -
Rwork0.214 -
obs-84.6 %

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