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- PDB-3br0: Crystal Structure of the Complex of Malachite Green Bound to QacR... -

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Basic information

Entry
Database: PDB / ID: 3br0
TitleCrystal Structure of the Complex of Malachite Green Bound to QacR(E120Q), a Mutant of a Multidrug Binding Transcriptional Repressor
ComponentsHTH-type transcriptional regulator qacR
KeywordsTRANSCRIPTION / QacR / multidrug resistance / TetR / malachite green / 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
IMIDAZOLE / MALACHITE GREEN / HTH-type transcriptional regulator QacR
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 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
A: HTH-type transcriptional regulator qacR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,50017
Polymers45,8802
Non-polymers1,62015
Water1,49583
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)95,00134
Polymers91,7604
Non-polymers3,24130
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
Buried area16170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.157, 104.157, 97.982
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: C72A,E120Q,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.: 12 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MGR / MALACHITE GREEN


Mass: 329.458 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H25N2 / Comment: Antimicrobial*YM
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 3.34 Å3/Da / Density % sol: 63.22 %
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: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 8, 2005 / Details: KOHZU: 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: 2.4→35.7 Å / Num. all: 23093 / Num. obs: 23093 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1.7 / Redundancy: 7.2 % / Biso Wilson estimate: 48.87 Å2 / Rsym value: 0.085 / Net I/σ(I): 6.1
Reflection shellResolution: 2.4→2.55 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 1.7 / Num. unique all: 3362 / Rsym value: 0.435 / % 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: 2.42→35.69 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.915 / SU B: 7.933 / SU ML: 0.186 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.317 / ESU R Free: 0.248 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2609 1175 5.1 %RANDOM
Rwork0.21361 ---
all0.21601 21890 --
obs0.21601 21722 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.946 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å2-0.2 Å20 Å2
2---0.4 Å20 Å2
3---0.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.42→35.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3031 0 95 83 3209
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223177
X-RAY DIFFRACTIONr_bond_other_d0.0010.022070
X-RAY DIFFRACTIONr_angle_refined_deg1.0561.9654294
X-RAY DIFFRACTIONr_angle_other_deg0.82735072
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1935368
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.08226.013158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.12215568
X-RAY DIFFRACTIONr_dihedral_angle_4_deg31.243154
X-RAY DIFFRACTIONr_chiral_restr0.0620.2457
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023455
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02637
X-RAY DIFFRACTIONr_nbd_refined0.2010.2761
X-RAY DIFFRACTIONr_nbd_other0.1720.22045
X-RAY DIFFRACTIONr_nbtor_refined0.1850.21561
X-RAY DIFFRACTIONr_nbtor_other0.0860.21522
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2100
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2120.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1270.226
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3350.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.23422006
X-RAY DIFFRACTIONr_mcbond_other0.1312752
X-RAY DIFFRACTIONr_mcangle_it2.14842956
X-RAY DIFFRACTIONr_scbond_it1.95241575
X-RAY DIFFRACTIONr_scangle_it2.73261338
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.42→2.483 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 80 -
Rwork0.252 1600 -
obs--99.82 %

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