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- PDB-3br5: Crystal Structure of the Complex of Rhodamine 6G Bound to QacR(E9... -

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Basic information

Entry
Database: PDB / ID: 3br5
TitleCrystal Structure of the Complex of Rhodamine 6G Bound to QacR(E90Q), a Mutant of a Multidrug Binding Transcriptional Repressor
ComponentsHTH-type transcriptional regulator qacR
KeywordsTRANSCRIPTION / QacR / multidrug resistance / TetR / Rhodamine 6G / 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
RHODAMINE 6G / HTH-type transcriptional regulator QacR
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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)94,82931
Polymers91,8884
Non-polymers2,94127
Water1629
1
B: HTH-type transcriptional regulator qacR
A: HTH-type transcriptional regulator qacR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,92519
Polymers45,9442
Non-polymers1,98117
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)46,90512
Polymers45,9442
Non-polymers96110
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)379,317124
Polymers367,55216
Non-polymers11,765108
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation2_445-x-1,-y-1,z1
crystal symmetry operation8_445-y-1,-x-1,-z1
crystal symmetry operation6_445x-1/2,-y-1/2,-z+1/21
crystal symmetry operation3_444-y-1/2,x-1/2,z-1/21
crystal symmetry operation5_445-x-1/2,y-1/2,-z+1/21
crystal symmetry operation4_444y-1/2,-x-1/2,z-1/21
Buried area59470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.726, 171.746, 94.785
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: 22972.000 Da / Num. of mol.: 4 / Mutation: E90Q,K67S,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.: 26 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-RHQ / RHODAMINE 6G


Mass: 443.557 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H31N2O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 3.8 Å3/Da / Density % sol: 67.66 %
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: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Aug 8, 2007
Details: Rosenbaum-Rock monochromator 1: high-resolution double-crystal sagittal focusing, Rosenbaum-Rock monochromator 2: double crystal, Rosenbaum-Rock vertical focusing mirror
RadiationMonochromator: Rosenbaum-Rock monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→49.03 Å / Num. obs: 31603 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1.9 / Redundancy: 7.52 % / Rsym value: 0.061 / Net I/σ(I): 18.1
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 7.45 % / Mean I/σ(I) obs: 1.9 / Num. unique all: 1517 / Rsym value: 0.4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CrystalCleardata collection
d*TREKdata reduction
d*TREKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1jt6

1jt6


Resolution: 2.9→49.03 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.889 / SU B: 16.59 / SU ML: 0.315 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.738 / ESU R Free: 0.379 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28449 1599 5.1 %RANDOM
Rwork0.24183 ---
all0.24395 30359 --
obs0.24395 30004 98.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 65.546 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.7 Å
Refinement stepCycle: LAST / Resolution: 2.9→49.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5856 0 196 9 6061
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0226157
X-RAY DIFFRACTIONr_bond_other_d0.0010.023825
X-RAY DIFFRACTIONr_angle_refined_deg0.9071.968375
X-RAY DIFFRACTIONr_angle_other_deg0.77539376
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9865737
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.54826.124307
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.63315990
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.451158
X-RAY DIFFRACTIONr_chiral_restr0.0490.2901
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026849
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021225
X-RAY DIFFRACTIONr_nbd_refined0.2160.21736
X-RAY DIFFRACTIONr_nbd_other0.160.24064
X-RAY DIFFRACTIONr_nbtor_refined0.1920.23158
X-RAY DIFFRACTIONr_nbtor_other0.0840.22975
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2156
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1470.233
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1490.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1030.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.78423751
X-RAY DIFFRACTIONr_mcbond_other0.05421504
X-RAY DIFFRACTIONr_mcangle_it1.46545856
X-RAY DIFFRACTIONr_scbond_it0.97243001
X-RAY DIFFRACTIONr_scangle_it1.58362519
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 121 -
Rwork0.322 2204 -
obs--99.44 %

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