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- PDB-3br3: Crystal Structure of the Complex of Ethidium Bound to QacR(E90Q),... -

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Basic information

Entry
Database: PDB / ID: 3br3
TitleCrystal Structure of the Complex of Ethidium Bound to QacR(E90Q), a Mutant of a Multidrug Binding Transcriptional Repressor
ComponentsHTH-type transcriptional regulator qacR
KeywordsTRANSCRIPTION / QacR / multidrug resistance / TetR / ethidium / DNA-binding / 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
ETHIDIUM / HTH-type transcriptional regulator QacR
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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: Advisory / 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
A: HTH-type transcriptional regulator qacR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,96311
Polymers45,8802
Non-polymers1,0839
Water27015
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
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)93,92622
Polymers91,7604
Non-polymers2,16618
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
Buried area13010 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: 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.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ET / ETHIDIUM


Mass: 314.404 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H20N3
#4: Water ChemComp-HOH / 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: 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: Jun 15, 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→46.04 Å / Num. all: 15047 / Num. obs: 15047 / % 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): 7.3
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: 2.8→41 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.898 / SU B: 30.927 / SU ML: 0.295 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 1.1 / ESU R Free: 0.412 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29326 702 5.1 %RANDOM
Rwork0.21844 ---
all0.22182 14276 --
obs0.22182 13187 92.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.77 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20.11 Å20 Å2
2--0.22 Å20 Å2
3----0.33 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å1.1 Å
Refinement stepCycle: LAST / Resolution: 2.8→41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2961 0 64 15 3040
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0223079
X-RAY DIFFRACTIONr_bond_other_d0.0010.021980
X-RAY DIFFRACTIONr_angle_refined_deg0.81.9554172
X-RAY DIFFRACTIONr_angle_other_deg0.7533.0014835
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3845365
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.65525.894151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.12915528
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.273154
X-RAY DIFFRACTIONr_chiral_restr0.0450.2451
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.023392
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02611
X-RAY DIFFRACTIONr_nbd_refined0.2040.2768
X-RAY DIFFRACTIONr_nbd_other0.150.21881
X-RAY DIFFRACTIONr_nbtor_refined0.1860.21569
X-RAY DIFFRACTIONr_nbtor_other0.0820.21426
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.266
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0950.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1350.223
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0460.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.67621878
X-RAY DIFFRACTIONr_mcbond_other0.0572748
X-RAY DIFFRACTIONr_mcangle_it1.26642921
X-RAY DIFFRACTIONr_scbond_it1.00541470
X-RAY DIFFRACTIONr_scangle_it1.60961251
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 52 -
Rwork0.253 1050 -
obs--98.66 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
117.01633.33980.275112.8674-1.34760.16530.5093-0.4793-1.42330.121-0.7805-0.50890.35230.09820.27120.18570.0054-0.02010.14640.11280.316859.133-14.35811.023
25.147-0.2778-0.30852.43070.32780.84560.0528-0.2881-0.25740.2029-0.2194-0.0203-0.1530.06850.16660.4491-0.0549-0.03010.3878-0.08810.285532.12-7.5511.178
38.8512.1490.62213.8672-1.89855.9166-0.30360.6551-0.4062-0.8820.0915-0.83120.69441.22170.21210.5648-0.04870.15620.5519-0.17870.334749.808-15.553-17.833
43.5635-0.9601-0.24991.92680.7792.6154-0.16920.48960.1251-0.4610.03890.0912-0.36130.10980.13020.4724-0.0859-0.11860.4502-0.12560.307326.782-7.466-8.768
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AB3 - 473 - 47
2X-RAY DIFFRACTION2AB48 - 18748 - 187
3X-RAY DIFFRACTION3BA4 - 474 - 47
4X-RAY DIFFRACTION4BA48 - 18748 - 187

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