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- PDB-3btj: crystal structure of QacR(E58Q) bound to dequalinium -

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Basic information

Entry
Database: PDB / ID: 3btj
Titlecrystal structure of QacR(E58Q) bound to dequalinium
ComponentsHTH-type transcriptional regulator qacR
KeywordsTRANSCRIPTION / QacR / multidrug binding / Dequalinium / bivalent drug / DNA-binding / Plasmid / Repressor / Transcription regulation
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
DEQUALINIUM / HTH-type transcriptional regulator QacR
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus Mu50 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.98 Å
AuthorsSchumacher, M.A. / Schuman, J.T. / Brennan, R.G.
CitationJournal: Biochemistry / Year: 2008
Title: QacR-cation recognition is mediated by a redundancy of residues capable of charge neutralization
Authors: Peters, K.M. / Schuman, J.T. / Skurray, R.A. / Brown, M.H. / Brennan, R.G. / Schumacher, M.A.
History
DepositionDec 28, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Source and taxonomy
Category: database_2 / entity_src_gen ...database_2 / entity_src_gen / 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 / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / 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
D: HTH-type transcriptional regulator qacR
A: HTH-type transcriptional regulator qacR
E: HTH-type transcriptional regulator qacR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,70222
Polymers88,6134
Non-polymers2,09018
Water1086
1
B: HTH-type transcriptional regulator qacR
A: HTH-type transcriptional regulator qacR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,43510
Polymers44,3062
Non-polymers1,1298
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: HTH-type transcriptional regulator qacR
E: HTH-type transcriptional regulator qacR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,26712
Polymers44,3062
Non-polymers96110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: HTH-type transcriptional regulator qacR
E: HTH-type transcriptional regulator qacR
hetero molecules

D: HTH-type transcriptional regulator qacR
E: HTH-type transcriptional regulator qacR
hetero molecules

D: HTH-type transcriptional regulator qacR
E: HTH-type transcriptional regulator qacR
hetero molecules

D: HTH-type transcriptional regulator qacR
E: HTH-type transcriptional regulator qacR
hetero molecules

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

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

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

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


Theoretical massNumber of molelcules
Total (without water)362,80988
Polymers354,45016
Non-polymers8,35972
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation7_556y,x,-z+11
crystal symmetry operation8_556-y,-x,-z+11
crystal symmetry operation3_455-y-1/2,x+1/2,z+1/21
crystal symmetry operation4_545y+1/2,-x-1/2,z+1/21
crystal symmetry operation5_455-x-1/2,y+1/2,-z+1/21
crystal symmetry operation6_545x+1/2,-y-1/2,-z+1/21
Buried area62910 Å2
ΔGint-1202.5 kcal/mol
Surface area119540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.900, 171.900, 94.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein
HTH-type transcriptional regulator qacR


Mass: 22153.156 Da / Num. of mol.: 4 / Mutation: E58Q,C72A,C141S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus Mu50 (bacteria)
Strain: Mu50 / Gene: qacR / Plasmid: PQE / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0A0N3
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-DEQ / DEQUALINIUM / DEQUADIN / Dequalinium


Mass: 456.665 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H40N4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 3.94 Å3/Da / Density % sol: 68.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: Ammonium sulphate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.03 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Apr 11, 2004 / Details: mirrors
RadiationMonochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 2.98→81.7 Å / Num. all: 29400 / Num. obs: 29386 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Biso Wilson estimate: 0.1 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.07 / Net I/σ(I): 9.3
Reflection shellResolution: 2.98→3.12 Å / Redundancy: 8 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.2 / Num. unique all: 500 / Rsym value: 0.432 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
CrystalCleardata collection
d*TREKdata reduction
d*TREKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1jt6

1jt6


Resolution: 2.98→76.88 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 2245768.44 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.264 1439 4.9 %RANDOM
Rwork0.216 ---
obs0.216 29331 99.3 %-
all-29386 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.7779 Å2 / ksol: 0.355302 e/Å3
Displacement parametersBiso mean: 72 Å2
Baniso -1Baniso -2Baniso -3
1-4.17 Å20 Å20 Å2
2--4.17 Å20 Å2
3----8.34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.69 Å0.55 Å
Luzzati d res low-5 Å
Luzzati sigma a0.71 Å0.66 Å
Refinement stepCycle: LAST / Resolution: 2.98→76.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6188 0 119 6 6313
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d18.2
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_mcbond_it5.151.5
X-RAY DIFFRACTIONc_mcangle_it7.62
X-RAY DIFFRACTIONc_scbond_it8.032
X-RAY DIFFRACTIONc_scangle_it11.112.5
LS refinement shellResolution: 2.98→3.17 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.478 267 5.7 %
Rwork0.444 4428 -
obs-344 97.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3deq_param.txtdeq_top.txt
X-RAY DIFFRACTION4ion.paramion.top

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