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- PDB-1jt6: Crystal structure of the multidrug binding protein QacR bound to ... -

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Basic information

Entry
Database: PDB / ID: 1jt6
TitleCrystal structure of the multidrug binding protein QacR bound to dequalinium
ComponentsHypothetical transcriptional regulator IN QACA 5'region
KeywordsTRANSCRIPTION / mutlidrug binding recognition / QacR / Mulitdrug resistance / S. aureus
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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.54 Å
AuthorsSchumacher, M.A. / Miller, M.C. / Grkovic, S. / Brown, M.H. / Skurray, R.A. / Brennan, R.G.
CitationJournal: Science / Year: 2001
Title: Structural mechanisms of QacR induction and multidrug recognition.
Authors: Schumacher, M.A. / Miller, M.C. / Grkovic, S. / Brown, M.H. / Skurray, R.A. / Brennan, R.G.
History
DepositionAug 20, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2001Provider: repository / Type: Initial release
Revision 1.1May 5, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: 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 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Apr 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: Hypothetical transcriptional regulator IN QACA 5'region
D: Hypothetical transcriptional regulator IN QACA 5'region
A: Hypothetical transcriptional regulator IN QACA 5'region
E: Hypothetical transcriptional regulator IN QACA 5'region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,76333
Polymers88,6174
Non-polymers3,14629
Water2,468137
1
B: Hypothetical transcriptional regulator IN QACA 5'region
A: Hypothetical transcriptional regulator IN QACA 5'region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,20618
Polymers44,3082
Non-polymers1,89816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6290 Å2
ΔGint-160 kcal/mol
Surface area18080 Å2
MethodPISA
2
D: Hypothetical transcriptional regulator IN QACA 5'region
E: Hypothetical transcriptional regulator IN QACA 5'region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,55715
Polymers44,3082
Non-polymers1,24913
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5560 Å2
ΔGint-198 kcal/mol
Surface area18000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.000, 172.000, 94.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
DetailsQacR is a dimer and there are two dimers in the asymmetric unit

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Components

#1: Protein
Hypothetical transcriptional regulator IN QACA 5'region / QACR REPRESSOR / ORF 188


Mass: 22154.143 Da / Num. of mol.: 4 / Mutation: C72A, C141S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Plasmid: pSK5210 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5a / References: UniProt: P0A0N4
#2: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-DEQ / DEQUALINIUM / DEQUADIN


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


Mass: 18.015 Da / Num. of mol.: 137 / 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: 3.95 Å3/Da / Density % sol: 68.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Ammonium sulphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.98 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 29, 2000 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.54→86 Å / Num. all: 55291 / Num. obs: 50664 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 65 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.064 / Net I/σ(I): 9
Reflection shellResolution: 2.54→2.61 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.1 / Num. unique all: 6998 / Rsym value: 0.41 / % possible all: 100

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Processing

Software
NameVersionClassification
CNSrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: QacR-R6G structure minus R6G

Resolution: 2.54→86 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1917643.65 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.256 4733 10.1 %RANDOM
Rwork0.209 ---
obs0.209 37103 99.5 %-
all-47041 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 69.1145 Å2 / ksol: 0.361951 e/Å3
Displacement parametersBiso mean: 71.6 Å2
Baniso -1Baniso -2Baniso -3
1-4.66 Å20 Å20 Å2
2--4.66 Å20 Å2
3----9.33 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.54→86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6188 0 174 137 6499
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d20.1
X-RAY DIFFRACTIONc_improper_angle_d1.01
X-RAY DIFFRACTIONc_mcbond_it2.91.5
X-RAY DIFFRACTIONc_mcangle_it4.472
X-RAY DIFFRACTIONc_scbond_it4.582
X-RAY DIFFRACTIONc_scangle_it6.722.5
LS refinement shellResolution: 2.54→2.7 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.381 750 9.7 %
Rwork0.335 6998 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5UNK_par-2.txtUNK_TOP.txt

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