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- PDB-1jup: Crystal structure of the multidrug binding transcriptional repres... -

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Basic information

Entry
Database: PDB / ID: 1jup
TitleCrystal structure of the multidrug binding transcriptional repressor QacR bound to malachite green
ComponentsHYPOTHETICAL TRANSCRIPTIONAL REGULATOR IN QACA 5'REGION
KeywordsTRANSCRIPTION / multidrug recognition / malachite green / 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 ...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
MALACHITE GREEN / HTH-type transcriptional regulator QacR
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.95 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 24, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 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 1.5Aug 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

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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)94,37527
Polymers91,9324
Non-polymers2,44323
Water1267
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)47,25613
Polymers45,9662
Non-polymers1,29011
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5820 Å2
ΔGint-133 kcal/mol
Surface area18020 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)47,11914
Polymers45,9662
Non-polymers1,15312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4790 Å2
ΔGint-147 kcal/mol
Surface area17840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.200, 174.200, 96.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
DetailsQacR is a dimer and there are two QacR dimers in the ASU one bound with the determined drug binding stoichiometry of one drug per dimer

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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: pSK5210 / 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.: 22 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 3.97 Å3/Da / Density % sol: 69.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Ammonium sulphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 23, 2000 / Details: yale mirrors
RadiationMonochromator: monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.95→64.6 Å / Num. all: 26023 / Num. obs: 26023 / % possible obs: 86.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 47.3 Å2 / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/σ(I): 11
Reflection shellResolution: 2.95→3.1 Å / Mean I/σ(I) obs: 2.4 / Rsym value: 0.278 / % possible all: 78

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Processing

Software
NameClassification
CNSrefinement
bioteXdata reduction
bioteXdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JUS

1jus


Resolution: 2.95→64.6 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1038053.03 / 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
Rfree0.281 2580 9.9 %RANDOM
Rwork0.238 ---
obs0.238 26023 81.9 %-
all-26023 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.9022 Å2 / ksol: 0.331763 e/Å3
Displacement parametersBiso mean: 65 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20 Å2
2--0.11 Å20 Å2
3----0.21 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.79 Å0.83 Å
Refinement stepCycle: LAST / Resolution: 2.95→64.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6188 0 135 7 6330
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d20.2
X-RAY DIFFRACTIONc_improper_angle_d0.93
X-RAY DIFFRACTIONc_mcbond_it1.441.5
X-RAY DIFFRACTIONc_mcangle_it2.582
X-RAY DIFFRACTIONc_scbond_it2.312
X-RAY DIFFRACTIONc_scangle_it3.642.5
LS refinement shellResolution: 2.95→3.13 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.371 221 9.4 %
Rwork0.374 2127 -
obs--45.3 %
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 DIFFRACTION5MGR_PAR.TXTMGR_TOP.TXT

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