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- PDB-2gby: Structure of QacR Multidrug Transcriptional Regulator Bound to Bi... -

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Basic information

Entry
Database: PDB / ID: 2gby
TitleStructure of QacR Multidrug Transcriptional Regulator Bound to Bivalent Diamidine Berenil
ComponentsHTH-type transcriptional regulator qacR
KeywordsTRANSCRIPTION / Diamidine / helix-turn-helix / multridrug binding
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
BERENIL / HTH-type transcriptional regulator QacR
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.9 Å
AuthorsSchuman, J.T.
CitationJournal: To be Published
Title: Structure of QacR Multidrug Transcriptional Regulator Bound to Trivalent and Bivalent Diamidine Drugs
Authors: Brennan, R.G. / Schuman, J.T.
History
DepositionMar 12, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 20, 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 1.3Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)93,27016
Polymers91,9324
Non-polymers1,33812
Water1448
1
B: HTH-type transcriptional regulator qacR
A: HTH-type transcriptional regulator qacR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8249
Polymers45,9662
Non-polymers8587
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4900 Å2
ΔGint-81 kcal/mol
Surface area17820 Å2
MethodPISA, PQS
2
D: HTH-type transcriptional regulator qacR
E: HTH-type transcriptional regulator qacR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4467
Polymers45,9662
Non-polymers4805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-83 kcal/mol
Surface area17390 Å2
MethodPISA, PQS
3
D: HTH-type transcriptional regulator qacR
hetero molecules

D: HTH-type transcriptional regulator qacR
hetero molecules

D: HTH-type transcriptional regulator qacR
hetero molecules

D: HTH-type transcriptional regulator qacR
hetero molecules

B: HTH-type transcriptional regulator qacR
A: HTH-type transcriptional regulator qacR
E: HTH-type transcriptional regulator qacR
hetero molecules

B: HTH-type transcriptional regulator qacR
A: HTH-type transcriptional regulator qacR
E: HTH-type transcriptional regulator qacR
hetero molecules

B: HTH-type transcriptional regulator qacR
A: HTH-type transcriptional regulator qacR
E: HTH-type transcriptional regulator qacR
hetero molecules

B: 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)373,08064
Polymers367,72816
Non-polymers5,35248
Water21612
TypeNameSymmetry operationNumber
crystal symmetry operation3_444-y-1/2,x-1/2,z-1/21
crystal symmetry operation4_444y-1/2,-x-1/2,z-1/21
crystal symmetry operation5_445-x-1/2,y-1/2,-z+1/21
crystal symmetry operation6_445x-1/2,-y-1/2,-z+1/21
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,-y-1,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_445-y-1,-x-1,-z1
Buried area49990 Å2
ΔGint-758 kcal/mol
Surface area125980 Å2
MethodPISA
4
B: HTH-type transcriptional regulator qacR
A: HTH-type transcriptional regulator qacR
hetero molecules

B: HTH-type transcriptional regulator qacR
A: HTH-type transcriptional regulator qacR
hetero molecules

B: HTH-type transcriptional regulator qacR
A: HTH-type transcriptional regulator qacR
hetero molecules

B: HTH-type transcriptional regulator qacR
A: HTH-type transcriptional regulator qacR
hetero molecules

D: HTH-type transcriptional regulator qacR
E: HTH-type transcriptional regulator qacR
hetero molecules

D: HTH-type transcriptional regulator qacR
E: HTH-type transcriptional regulator qacR
hetero molecules

D: HTH-type transcriptional regulator qacR
E: HTH-type transcriptional regulator qacR
hetero molecules

D: HTH-type transcriptional regulator qacR
E: HTH-type transcriptional regulator qacR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)373,08064
Polymers367,72816
Non-polymers5,35248
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,-y-1,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_445-y-1,-x-1,-z1
crystal symmetry operation3_444-y-1/2,x-1/2,z-1/21
crystal symmetry operation4_444y-1/2,-x-1/2,z-1/21
crystal symmetry operation5_445-x-1/2,y-1/2,-z+1/21
crystal symmetry operation6_445x-1/2,-y-1/2,-z+1/21
Buried area54720 Å2
ΔGint-778 kcal/mol
Surface area121260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.340, 171.340, 94.530
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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: qacR / Production host: Escherichia coli (E. coli) / References: UniProt: P0A0N4
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-BRN / BERENIL / DIMINAZINE ACETURATE / 1,3-TRIS-(4'AMIDINOPHENYL)TRIAZINE


Mass: 281.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H15N7 / Comment: medication*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 3.77 Å3/Da / Density % sol: 67.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: 3M ammonium sulfate and 1M sodium acetate, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.078 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Jun 6, 2004
RadiationMonochromator: fiber optic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.078 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. obs: 31538 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 5.82 % / Biso Wilson estimate: 42.36 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.1
Reflection shellResolution: 2.9→3 Å / Redundancy: 5.65 % / Rmerge(I) obs: 0.308 / Mean I/σ(I) obs: 3.8 / Num. unique all: 31667 / % possible all: 9.4

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Processing

Software
NameClassification
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.9→30 Å / Cross valid method: THROUGHOUT / σ(F): 2.938 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.29 28429 -Maximum likelihood
Rwork0.2487 ---
obs0.2487 31538 100 %-
all-31714 --
Refinement stepCycle: LAST / Resolution: 2.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6188 0 76 8 6272
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_mcbond_it1.53
X-RAY DIFFRACTIONc_mcangle_it2.75

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