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- PDB-3pm1: Structure of QacR E90Q bound to Ethidium -

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Basic information

Entry
Database: PDB / ID: 3pm1
TitleStructure of QacR E90Q bound to Ethidium
ComponentsHTH-type transcriptional regulator qacR
KeywordsTRANSCRIPTION / TetR family member / transcription regulation / multidrug resistance / DNA / nucleoid
Function / homology
Function and homology information


DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Transcription regulator QacR, C-terminal / QacR-like protein, 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 QacR, C-terminal / QacR-like protein, 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. / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ETHIDIUM / HTH-type transcriptional regulator QacR
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsSchumacher, M.A.
CitationJournal: Plos One / Year: 2011
Title: A single acidic residue can guide binding site selection but does not govern QacR cationic-drug affinity.
Authors: Peters, K.M. / Brooks, B.E. / Schumacher, M.A. / Skurray, R.A. / Brennan, R.G. / Brown, M.H.
History
DepositionNov 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 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
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: HTH-type transcriptional regulator qacR
A: HTH-type transcriptional regulator qacR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,86710
Polymers45,8802
Non-polymers9878
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5060 Å2
ΔGint-95 kcal/mol
Surface area18200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.148, 104.148, 98.564
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

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Components

#1: Protein HTH-type transcriptional regulator qacR


Mass: 22939.936 Da / Num. of mol.: 2 / Mutation: K67S, C72A, E90Q, C141S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: Mu50 / Gene: qacR / Plasmid: pet / Production host: Escherichia coli (E. coli) / Strain (production host): DH5[alpha] / References: UniProt: P0A0N3
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ET / ETHIDIUM / Ethidium bromide


Mass: 314.404 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H20N3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 3.36 Å3/Da / Density % sol: 63.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: ammonium sulfate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorDate: Apr 23, 2005
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→41 Å / Num. obs: 13889 / % possible obs: 92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 43.3 Å2
Reflection shellResolution: 2.8→2.98 Å / % possible all: 92

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
CNS1.2refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3RB2

3rb2


Resolution: 2.8→34.09 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2313508.34 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.28 1410 10.2 %RANDOM
Rwork0.229 ---
obs0.229 13889 92.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.2558 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 70.6 Å2
Baniso -1Baniso -2Baniso -3
1-3.81 Å20 Å20 Å2
2--3.81 Å20 Å2
3----7.61 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.46 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.8→34.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3078 0 59 15 3152
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d17.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.471.5
X-RAY DIFFRACTIONc_mcangle_it2.572
X-RAY DIFFRACTIONc_scbond_it1.972
X-RAY DIFFRACTIONc_scangle_it3.142.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.345 224 9.2 %
Rwork0.277 2224 -
obs--97.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION5et.param.txtet.top

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