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- PDB-1jt0: Crystal structure of a cooperative QacR-DNA complex -

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Basic information

Entry
Database: PDB / ID: 1jt0
TitleCrystal structure of a cooperative QacR-DNA complex
Components
  • HYPOTHETICAL TRANSCRIPTIONAL REGULATOR IN QACA 5'REGION
  • QACA operator
KeywordsTRANSCRIPTION/DNA / multidrug binding protein / cooperative DNA binding / dimer of dimers / TRANSCRIPTION-DNA COMPLEX
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
DNA / DNA (> 10) / HTH-type transcriptional regulator QacR
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.9 Å
AuthorsSchumacher, M.A. / Miller, M.C. / Grkovic, S. / Brown, M.H. / Skurray, R.A. / Brennan, R.G.
CitationJournal: EMBO J. / Year: 2002
Title: Structural basis for cooperative DNA binding by two dimers of the multidrug-binding protein QacR.
Authors: Schumacher, M.A. / Miller, M.C. / Grkovic, S. / Brown, M.H. / Skurray, R.A. / Brennan, R.G.
History
DepositionAug 20, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 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 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: QACA operator
F: QACA operator
A: HYPOTHETICAL TRANSCRIPTIONAL REGULATOR IN QACA 5'REGION
B: HYPOTHETICAL TRANSCRIPTIONAL REGULATOR IN QACA 5'REGION
C: HYPOTHETICAL TRANSCRIPTIONAL REGULATOR IN QACA 5'REGION
D: HYPOTHETICAL TRANSCRIPTIONAL REGULATOR IN QACA 5'REGION
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,62211
Polymers109,1416
Non-polymers4805
Water81145
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)174.700, 174.700, 151.950
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Detailsthe entire QacR dimer of dimer - DNA complex is contained within the crystallographic asymmetric unit

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Components

#1: DNA chain QACA operator


Mass: 8604.564 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein
HYPOTHETICAL TRANSCRIPTIONAL REGULATOR IN QACA 5'REGION / QacR repressor / ORF 188


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) / Plasmid: pSK5210 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5a / References: UniProt: P0A0N4
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 6.13 Å3/Da / Density % sol: 79.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Lithium sulphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutionsName: Li2(SO4)
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
1100 %satlithium sulfate1reservoir
210 mMmagnesium sulfate1reservoir
30.1 MHEPES1reservoirpH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 23, 2000 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.9→75.73 Å / Num. all: 59396 / Num. obs: 59396 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 144.8 Å2 / Rmerge(I) obs: 0.054 / Rsym value: 0.06 / Net I/σ(I): 11.4
Reflection shellResolution: 2.9→3.03 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.527 / Mean I/σ(I) obs: 1.7 / Num. unique all: 4414 / Rsym value: 0.52 / % possible all: 99.9
Reflection
*PLUS
Num. measured all: 302270
Reflection shell
*PLUS
Highest resolution: 2.9 Å / Rmerge(I) obs: 0.401 / Mean I/σ(I) obs: 1.8

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MIR / Resolution: 2.9→75.73 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 12802447.79 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.258 5846 10.2 %RANDOM
Rwork0.222 ---
all0.217 57542 --
obs0.222 57542 98.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 86.0326 Å2 / ksol: 0.373149 e/Å3
Displacement parametersBiso mean: 81.5 Å2
Baniso -1Baniso -2Baniso -3
1-7.87 Å219.26 Å20 Å2
2--7.87 Å20 Å2
3----15.74 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.65 Å0.6 Å
Refinement stepCycle: LAST / Resolution: 2.9→75.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6239 1142 25 45 7451
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d19.6
X-RAY DIFFRACTIONc_improper_angle_d1.06
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.393 973 10.1 %
Rwork0.363 8690 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Refinement
*PLUS
Lowest resolution: 75.7 Å / σ(F): 0 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 81.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.36
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.06
LS refinement shell
*PLUS
Rfactor Rfree: 0.393 / % reflection Rfree: 10.1 % / Rfactor Rwork: 0.363

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