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- PDB-3br6: Crystal Structure of the Complex of Rhodamine 6G Bound to QacR(E1... -

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Basic information

Entry
Database: PDB / ID: 3br6
TitleCrystal Structure of the Complex of Rhodamine 6G Bound to QacR(E120Q), a Mutant of a Multidrug Binding Transcriptional Repressor
ComponentsHTH-type transcriptional regulator qacR
KeywordsTRANSCRIPTION / QacR / multidrug resistance / TetR / Rhodamine 6G / 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
RHODAMINE 6G / HTH-type transcriptional regulator QacR
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 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
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)94,02824
Polymers91,7604
Non-polymers2,26920
Water543
1
B: HTH-type transcriptional regulator qacR
A: HTH-type transcriptional regulator qacR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9009
Polymers45,8802
Non-polymers1,0207
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)47,12915
Polymers45,8802
Non-polymers1,24913
Water181
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)376,11496
Polymers367,03916
Non-polymers9,07580
Water21612
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 area56390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.099, 173.099, 95.576
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: 22939.936 Da / Num. of mol.: 4 / Mutation: E120Q,K67S,C72A,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.: 19 / 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.: 3 / 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: 3.9 Å3/Da / Density % sol: 68.47 %
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 3, 2005 / Details: Rosenbaum-Rock monochromator
RadiationMonochromator: Rosenbaum-Rock monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→49.4 Å / Num. all: 24505 / Num. obs: 22888 / % possible obs: 93.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1.5 / Redundancy: 5.16 % / Rsym value: 0.059 / Net I/σ(I): 6.7
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 0.5 / Num. unique all: 2324 / Rsym value: 0.62 / % possible all: 99.7

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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: 3.2→48 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.904 / SU B: 51.895 / SU ML: 0.4 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.493 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28286 1152 5 %RANDOM
Rwork0.2285 ---
all0.23118 23264 --
obs0.23118 21706 93.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 100.356 Å2
Baniso -1Baniso -2Baniso -3
1-1.03 Å20 Å20 Å2
2--1.03 Å20 Å2
3----2.05 Å2
Refine analyzeLuzzati coordinate error free: 0.5 Å
Refinement stepCycle: LAST / Resolution: 3.2→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5812 0 128 3 5943
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0226044
X-RAY DIFFRACTIONr_bond_other_d0.0010.023790
X-RAY DIFFRACTIONr_angle_refined_deg0.8941.9518207
X-RAY DIFFRACTIONr_angle_other_deg0.78939284
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8225730
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.3525.822292
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.78815978
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.674158
X-RAY DIFFRACTIONr_chiral_restr0.0490.2899
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.026708
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021217
X-RAY DIFFRACTIONr_nbd_refined0.2150.21659
X-RAY DIFFRACTIONr_nbd_other0.160.23842
X-RAY DIFFRACTIONr_nbtor_refined0.190.23106
X-RAY DIFFRACTIONr_nbtor_other0.0860.22935
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.2128
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1290.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1050.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0760.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.58923741
X-RAY DIFFRACTIONr_mcbond_other0.04121499
X-RAY DIFFRACTIONr_mcangle_it1.09245804
X-RAY DIFFRACTIONr_scbond_it0.80342789
X-RAY DIFFRACTIONr_scangle_it1.27762402
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.415 82 -
Rwork0.304 1613 -
obs--97.19 %
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)
16.429-1.75795.4863.96412.424417.385-0.07490.0230.21180.64920.14360.090.3640.4496-0.0687-0.72940.04070.0668-0.85010.0004-0.2722-53.835-58.2615.897
23.9265-2.0921.44935.3141-2.22553.04520.2032-0.09590.2487-0.0132-0.0821-0.0704-0.3338-0.1349-0.1211-0.77480.06740.114-0.8189-0.1223-0.3069-70.102-40.5952.007
36.52971.4231-4.76934.954.775316.5510.88890.8768-2.91810.8158-0.1439-0.22611.7805-0.3521-0.745-1.1084-0.1254-0.4127-0.98590.08370.2173-84.581-72.2679.518
45.4802-0.85010.56177.4685-2.07623.69150.39540.277-0.4122-0.3673-0.2120.0622-0.0667-0.2318-0.1834-1.03120.10430.055-0.7006-0.1814-0.3053-89.067-48.318-0.205
55.6977-0.0529-1.385315.36830.066111.8020.21710.53690.63271.0233-0.20620.8837-1.3774-0.3441-0.0109-0.7116-0.08390.0252-0.78950.0235-0.1877-36.827-28.82639.172
64.6161-0.5762-1.63012.73291.26472.81320.05050.64670.3012-0.1858-0.2422-0.0999-0.29790.31730.1918-0.992-0.0835-0.1555-0.5490.0973-0.2943-18.735-42.1525.554
712.12911.9883-0.68794.84821.557618.68170.1924-0.5885-0.05790.2824-0.30340.42760.9643-1.3940.111-0.7102-0.0963-0.0183-0.5828-0.1116-0.3395-49.738-54.54237.425
85.94030.4134-1.12082.1910.5494.00650.2314-0.0232-0.45820.2952-0.1653-0.21470.29980.605-0.0662-0.78850.0762-0.1185-0.6829-0.0755-0.3413-27.12-61.15125.737
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AC2 - 472 - 47
2X-RAY DIFFRACTION2AC48 - 18748 - 187
3X-RAY DIFFRACTION3BA3 - 473 - 47
4X-RAY DIFFRACTION4BA48 - 18748 - 187
5X-RAY DIFFRACTION5DB2 - 472 - 47
6X-RAY DIFFRACTION6DB48 - 18748 - 187
7X-RAY DIFFRACTION7ED2 - 472 - 47
8X-RAY DIFFRACTION8ED48 - 18748 - 187

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