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- PDB-3br1: Crystal Structure of the Complex of Dequalinium Bound to QacR(E90... -

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Basic information

Entry
Database: PDB / ID: 3br1
TitleCrystal Structure of the Complex of Dequalinium Bound to QacR(E90Q), a Mutant of a Multidrug Binding Transcriptional Repressor
ComponentsHTH-type transcriptional regulator qacR
KeywordsTRANSCRIPTION / QacR / multidrug resistance / TetR / dequalinium / 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 ...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 / MOLECULAR REPLACEMENT / Resolution: 3.31 Å
AuthorsBrooks, B.E.
CitationJournal: To be Published
Title: Formal electrostatic interactions do not govern QacR-cation affinity
Authors: Brooks, B.E. / Hardie, K.M. / Brown, M.H. / Skurray, R.A. / Brennan, R.G.
History
DepositionDec 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 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 1.3Aug 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)94,49827
Polymers91,9284
Non-polymers2,57023
Water36020
1
B: HTH-type transcriptional regulator qacR
A: HTH-type transcriptional regulator qacR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,38113
Polymers45,9642
Non-polymers1,41711
Water362
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)47,11714
Polymers45,9642
Non-polymers1,15312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
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

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


Theoretical massNumber of molelcules
Total (without water)377,993108
Polymers367,71316
Non-polymers10,28092
Water28816
TypeNameSymmetry operationNumber
crystal symmetry operation6_545x+1/2,-y-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 operation3_455-y-1/2,x+1/2,z+1/21
identity operation1_555x,y,z1
crystal symmetry operation8_556-y,-x,-z+11
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area59740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.226, 170.226, 93.577
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: 22982.037 Da / Num. of mol.: 4 / Mutation: C72S,E90Q,C141S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: Mu50 / Gene: qacR / Plasmid: pTTQ18 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5-alpha / References: UniProt: P0A0N3
#2: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 22 / 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.: 20 / 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: 3.69 Å3/Da / Density % sol: 66.64 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 1:1 10mg/ml protein with 2.3M Ammonium sulfate with 100mM Sodium Acetate pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 273K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 2, 2003 / Details: Double Crystal Si(111)
RadiationMonochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.31→82.06 Å / Num. obs: 21054 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 7 % / Rsym value: 0.079 / Net I/σ(I): 8.9
Reflection shellResolution: 3.31→3.49 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 2.01 / Num. unique all: 309 / Rsym value: 0.324 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
BOSdata collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1jt6

1jt6


Resolution: 3.31→73.92 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.847 / SU B: 21.7 / SU ML: 0.367 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.509 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27722 1081 5.1 %RANDOM
Rwork0.21924 ---
all0.22206 19973 --
obs0.22206 19973 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.505 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refine analyzeLuzzati coordinate error free: 0.5 Å
Refinement stepCycle: LAST / Resolution: 3.31→73.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5772 0 144 20 5936
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0226013
X-RAY DIFFRACTIONr_bond_other_d0.0010.023774
X-RAY DIFFRACTIONr_angle_refined_deg0.8231.958168
X-RAY DIFFRACTIONr_angle_other_deg0.76539238
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8395726
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.45125.822292
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.4715964
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.206158
X-RAY DIFFRACTIONr_chiral_restr0.0460.2888
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.026684
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021224
X-RAY DIFFRACTIONr_nbd_refined0.2160.21752
X-RAY DIFFRACTIONr_nbd_other0.1570.24130
X-RAY DIFFRACTIONr_nbtor_refined0.1910.23053
X-RAY DIFFRACTIONr_nbtor_other0.0840.22935
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2202
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1280.224
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1410.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1250.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.72923705
X-RAY DIFFRACTIONr_mcbond_other0.04121488
X-RAY DIFFRACTIONr_mcangle_it1.35945773
X-RAY DIFFRACTIONr_scbond_it0.78942706
X-RAY DIFFRACTIONr_scangle_it1.26462395
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.31→3.396 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 92 -
Rwork0.28 1436 -
obs--100 %

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