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- PDB-1jtx: Crystal structure of the multidrug binding transcriptional regula... -

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Basic information

Entry
Database: PDB / ID: 1jtx
TitleCrystal structure of the multidrug binding transcriptional regulator QacR bound to crystal violet
ComponentsHYPOTHETICAL TRANSCRIPTIONAL REGULATOR IN QACA 5'REGION
KeywordsTRANSCRIPTION / multidrug binding / repressor / S. aureus / QacA / QacR / multidrug recognition
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
CRYSTAL VIOLET / HTH-type transcriptional regulator QacR
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.85 Å
AuthorsSchumacher, M.A. / Miller, M.C. / Grkovic, S. / Brown, M.H. / Skurray, R.A. / Brennan, R.G.
CitationJournal: Science / Year: 2001
Title: Structural mechanisms of QacR induction and multidrug recognition.
Authors: Schumacher, M.A. / Miller, M.C. / Grkovic, S. / Brown, M.H. / Skurray, R.A. / Brennan, R.G.
History
DepositionAug 22, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2001Provider: 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 1.4Aug 16, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)94,61029
Polymers91,9324
Non-polymers2,67825
Water1,15364
1
B: HYPOTHETICAL TRANSCRIPTIONAL REGULATOR IN QACA 5'REGION
A: HYPOTHETICAL TRANSCRIPTIONAL REGULATOR IN QACA 5'REGION
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,58716
Polymers45,9662
Non-polymers1,62114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6060 Å2
ΔGint-154 kcal/mol
Surface area18110 Å2
MethodPISA
2
D: HYPOTHETICAL TRANSCRIPTIONAL REGULATOR IN QACA 5'REGION
E: HYPOTHETICAL TRANSCRIPTIONAL REGULATOR IN QACA 5'REGION
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,02313
Polymers45,9662
Non-polymers1,05711
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-151 kcal/mol
Surface area17940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.900, 172.900, 95.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
DetailsThe natural oligmeric state is a dimer- there are two dimers in the ASU

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Components

#1: 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: pSK / Production host: Escherichia coli (E. coli) / Strain (production host): DH5a / References: UniProt: P0A0N4
#2: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CVI / CRYSTAL VIOLET


Mass: 372.526 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H30N3 / Comment: antifungal, antibiotic*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 3.87 Å3/Da / Density % sol: 68.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Ammonium sulphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
1200 mMglycine1drop
215 mg/mlprotein1drop
325 mMTris1reservoirpH7.5
450 mMimidazole1drop
5300 mM1dropNaCl
65 %glycerol1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 20, 2000 / Details: mirrors
RadiationMonochromator: monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.85→63.97 Å / Num. all: 34304 / Num. obs: 34304 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.9 % / Biso Wilson estimate: 62.7 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.064 / Net I/σ(I): 8.5
Reflection shellResolution: 2.85→2.92 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.449 / Mean I/σ(I) obs: 1.7 / Num. unique all: 2508 / Rsym value: 0.449 / % possible all: 100
Reflection
*PLUS
Num. measured all: 340448 / Rmerge(I) obs: 0.064

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Processing

Software
NameVersionClassification
CNSrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1JUS

1jus


Resolution: 2.85→63.97 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1728986.14 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh and Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.284 3417 10 %RANDOM
Rwork0.227 ---
all-34220 --
obs-34220 100 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 65.2069 Å2 / ksol: 0.359843 e/Å3
Displacement parametersBiso mean: 77 Å2
Baniso -1Baniso -2Baniso -3
1-1.62 Å20 Å20 Å2
2--1.62 Å20 Å2
3----3.24 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.85→63.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6188 0 148 64 6400
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d19.2
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_mcbond_it2.451.5
X-RAY DIFFRACTIONc_mcangle_it4.092
X-RAY DIFFRACTIONc_scbond_it3.522
X-RAY DIFFRACTIONc_scangle_it5.52.5
LS refinement shellResolution: 2.85→3.03 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.398 556 9.9 %
Rwork0.354 5052 -
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
X-RAY DIFFRACTION5CVI.PARAMCV.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.228 / Rfactor Rfree: 0.286
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 77 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg2.43
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.84
X-RAY DIFFRACTIONc_mcbond_it2.451.5
X-RAY DIFFRACTIONc_scbond_it3.522
X-RAY DIFFRACTIONc_mcangle_it4.092
X-RAY DIFFRACTIONc_scangle_it5.52.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.398 / % reflection Rfree: 9.9 % / Rfactor Rwork: 0.354

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