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- PDB-2dtz: Crystal Structure of multidrug binding protein QacR from Staphylo... -

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Basic information

Entry
Database: PDB / ID: 2dtz
TitleCrystal Structure of multidrug binding protein QacR from Staphylococcus aureus cocrystallized with compound DB75
ComponentsHTH-type transcriptional regulator qacR
KeywordsTRANSCRIPTION / MULTIDRUG RECOGNITION / DB75 / QACR / MULTIDRUG BINDING PROTEIN
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 / TetR-type HTH domain profile. ...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
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. / Brennan, R.G.
CitationJournal: J.Am.Chem.Soc. / Year: 2007
Title: Multidrug-Binding Transcription Factor QacR Binds the Bivalent Aromatic Diamidines DB75 and DB359 in Multiple Positions
Authors: Brooks, B.E. / Piro, K.M. / Brennan, R.G.
History
DepositionJul 19, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 17, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 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 1.4Oct 25, 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)92,70112
Polymers91,9324
Non-polymers7698
Water41423
1
B: HTH-type transcriptional regulator qacR
A: HTH-type transcriptional regulator qacR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3506
Polymers45,9662
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-55 kcal/mol
Surface area17900 Å2
MethodPISA
2
D: HTH-type transcriptional regulator qacR
E: HTH-type transcriptional regulator qacR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3506
Polymers45,9662
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-69 kcal/mol
Surface area17520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.497, 171.497, 94.316
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: 22983.023 Da / Num. of mol.: 4 / Mutation: C72A, C141S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: QacR, SAVP031 / Plasmid: pttq18 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A0N4
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 3.76 Å3/Da / Density % sol: 67.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: Mother liquor consists of 2.3 -2.7M ammonium sulfate and 0.1M sodium acetate. The protein stock solution is 10mg/mL and is mixed with a 1:1 dilution with the mother liquor. The ligand is ...Details: Mother liquor consists of 2.3 -2.7M ammonium sulfate and 0.1M sodium acetate. The protein stock solution is 10mg/mL and is mixed with a 1:1 dilution with the mother liquor. The ligand is added to the protein stock solution at concentrations of 200-500 micromolar., pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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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 210 / Detector: CCD / Date: Dec 14, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→76.7 Å / Num. all: 35209 / Num. obs: 34470 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 52.8 Å2
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 2 / Num. unique all: 4828 / % possible all: 96.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1jt6

1jt6


Resolution: 2.8→76.7 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2688886.24 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: DB75 ligand is disordered. The A and B chains and D and E chains form two distinct dimers. The A and B dimer assumes the drug bound conformation. The D and E dimer assumes the apo conformation.
RfactorNum. reflection% reflectionSelection details
Rfree0.289 3435 10 %RANDOM
Rwork0.224 ---
obs0.224 34470 97.9 %-
all-35209 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.3873 Å2 / ksol: 0.334565 e/Å3
Displacement parametersBiso mean: 70.3 Å2
Baniso -1Baniso -2Baniso -3
1-5.83 Å20 Å20 Å2
2--5.83 Å20 Å2
3----11.67 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.55 Å0.49 Å
Refinement stepCycle: LAST / Resolution: 2.8→76.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6000 0 40 23 6063
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.404 566 10.3 %
Rwork0.361 4942 -
obs--96 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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