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

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Basic information

Entry
Database: PDB / ID: 1jus
TitleCrystal structure of the multidrug binding transcriptional repressor QacR bound to rhodamine 6G
ComponentsHYPOTHETICAL TRANSCRIPTIONAL REGULATOR IN QACA 5'REGION
KeywordsTRANSCRIPTION / multidrug recognition / S. aureus / QacR / Rhodamine 6G / cationic lipophilic drugs
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
RHODAMINE 6G / HTH-type transcriptional regulator QacR
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.84 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 27, 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 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)95,14828
Polymers92,4954
Non-polymers2,65324
Water1,11762
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)47,94016
Polymers46,2472
Non-polymers1,69214
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6090 Å2
ΔGint-157 kcal/mol
Surface area18140 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)47,20812
Polymers46,2472
Non-polymers96110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-150 kcal/mol
Surface area17700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.300, 172.300, 95.000
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 dimers in the ASU one drug bound and one drug free

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Components

#1: Protein
HYPOTHETICAL TRANSCRIPTIONAL REGULATOR IN QACA 5'REGION / QACR REPRESSOR / ORF 188


Mass: 23123.707 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.: 23 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-RHQ / RHODAMINE 6G


Mass: 443.557 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H31N2O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 3.81 Å3/Da / Density % sol: 67.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Ammonium sulphate,crystals were grown after the protein was reductively alkylated. All QacR-drug complexes were crystallized in this manner. Although not required, only small crystals are ...Details: Ammonium sulphate,crystals were grown after the protein was reductively alkylated. All QacR-drug complexes were crystallized in this manner. Although not required, only small crystals are obtained otherwise and take several months to grow., pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 24, 2000
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.84→83.2 Å / Num. all: 34367 / Num. obs: 34367 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 45.6 Å2 / Rsym value: 0.049 / Net I/σ(I): 10.5
Reflection shellResolution: 2.84→2.91 Å / Redundancy: 7 % / Mean I/σ(I) obs: 2.9 / Rsym value: 0.259 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNSrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.84→77.06 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 15564905.82 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh and huber
RfactorNum. reflection% reflectionSelection details
Rfree0.272 3424 10 %RANDOM
Rwork0.23 ---
obs-34321 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.4873 Å2 / ksol: 0.362825 e/Å3
Displacement parametersBiso mean: 68.7 Å2
Baniso -1Baniso -2Baniso -3
1-2.7 Å20 Å20 Å2
2--2.7 Å20 Å2
3----5.41 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.55 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 2.84→77.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6188 0 148 62 6398
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d19.1
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_mcbond_it1.591.5
X-RAY DIFFRACTIONc_mcangle_it2.832
X-RAY DIFFRACTIONc_scbond_it2.092
X-RAY DIFFRACTIONc_scangle_it3.472.5
LS refinement shellResolution: 2.83→3.01 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.414 517 9.6 %
Rwork0.354 4875 -
obs--94.8 %
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 DIFFRACTION5RHODA-NEW3.PARAMRHODA-NEW3.TOP

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