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- PDB-2qop: Crystal structure of the transcriptional regulator AcrR from Esch... -

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Basic information

Entry
Database: PDB / ID: 2qop
TitleCrystal structure of the transcriptional regulator AcrR from Escherichia coli
ComponentsHTH-type transcriptional regulator acrR
KeywordsTRANSCRIPTION / AcrB regulator / DNA-binding / Repressor / Transcription regulation
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 ...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 / MAD / Resolution: 2.55 Å
AuthorsLi, M. / Gu, R. / Su, C.-C. / McDermott, G. / Yu, E.W.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Crystal structure of the transcriptional regulator AcrR from Escherichia coli.
Authors: Li, M. / Gu, R. / Su, C.C. / Routh, M.D. / Harris, K.C. / Jewell, E.S. / McDermott, G. / Yu, E.W.
History
DepositionJul 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 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


Theoretical massNumber of molelcules
Total (without water)24,7981
Polymers24,7981
Non-polymers00
Water63135
1
A: HTH-type transcriptional regulator acrR

A: HTH-type transcriptional regulator acrR


Theoretical massNumber of molelcules
Total (without water)49,5952
Polymers49,5952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area4020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.218, 54.574, 73.726
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221
DetailsThe dimer is generated by space group p2221

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Components

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


Mass: 24797.658 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12 / 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.: 35 / 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: 1.96 Å3/Da / Density % sol: 37.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 35% PEG 4000, 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: ALS / Beamline: 8.2.2 / Wavelength: 0.979249 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 15, 2006
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979249 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 6766 / % possible obs: 98.2 % / Observed criterion σ(F): 3.3 / Observed criterion σ(I): 3.3 / Redundancy: 6.9 % / Rmerge(I) obs: 0.076 / Rsym value: 0.074 / Net I/σ(I): 22
Reflection shellResolution: 2.55→2.64 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.306 / Mean I/σ(I) obs: 3.3 / Num. unique all: 1041 / Rsym value: 0.24 / % possible all: 85.2

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Processing

Software
NameClassification
HKL-2000data collection
SnBphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.55→50 Å / Isotropic thermal model: Isotropic / σ(F): 4 / σ(I): 4
RfactorNum. reflection% reflectionSelection details
Rfree0.273 250 -random
Rwork0.228 ---
all-5982 --
obs-5085 85.2 %-
Displacement parametersBiso mean: 54 Å2
Refinement stepCycle: LAST / Resolution: 2.55→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1672 0 0 35 1707
Refine LS restraintsType: p_bond_d / Dev ideal: 0.022

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