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- PDB-5ffz: S. aureus MepR bound to ethidium bromide -

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Basic information

Entry
Database: PDB / ID: 5ffz
TitleS. aureus MepR bound to ethidium bromide
ComponentsMarR family regulatory protein
KeywordsTRANSCRIPTION / Winged helix-turn-helix / protein-ligand complex / transcription regulation / multidrug resistance / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


response to stress / DNA-binding transcription factor activity
Similarity search - Function
MarR family / : / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ETHIDIUM / : / MarR family regulatory protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.585 Å
AuthorsBirukou, I. / Newman, C.E. / Brennan, R.G.
CitationJournal: To Be Published
Title: S. aureus MepR bound to ethidium bromide
Authors: Birukou, I. / Newman, C.E. / Brennan, R.G.
History
DepositionDec 19, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MarR family regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6163
Polymers16,2621
Non-polymers3542
Water1629
1
A: MarR family regulatory protein
hetero molecules

A: MarR family regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2326
Polymers32,5252
Non-polymers7074
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_765-x+8/3,-x+y+4/3,-z+1/31
Buried area3520 Å2
ΔGint-39 kcal/mol
Surface area15830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.061, 119.061, 56.279
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-405-

HOH

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Components

#1: Protein MarR family regulatory protein / MarR family transcriptional regulator / MepA/mepB repressor and autoregulator / MepR


Mass: 16262.288 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: mepR / Production host: Escherichia coli (E. coli) / References: UniProt: Q5Y812
#2: Chemical ChemComp-ET / ETHIDIUM


Mass: 314.404 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H20N3
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.36 Å3/Da / Density % sol: 47.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 4M potassium formate, 0.1 M BisTris propane, pH 9, 2% PEG MME 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Apr 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.5848→50 Å / Num. obs: 4865 / % possible obs: 99.37 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 19.32
Reflection shellResolution: 2.5848→2.64 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.461 / Mean I/σ(I) obs: 3.08 / % possible all: 93.93

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3eco

3eco


Resolution: 2.585→38.015 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2699 486 10.01 %random selection
Rwork0.2453 ---
obs0.2479 4857 99.2 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.585→38.015 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1017 0 25 9 1051
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041057
X-RAY DIFFRACTIONf_angle_d0.8741439
X-RAY DIFFRACTIONf_dihedral_angle_d15.191355
X-RAY DIFFRACTIONf_chiral_restr0.032168
X-RAY DIFFRACTIONf_plane_restr0.005185
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5848-2.95870.38821580.33421421X-RAY DIFFRACTION98
2.9587-3.72710.341610.28761455X-RAY DIFFRACTION100
3.7271-38.01950.22971670.21791495X-RAY DIFFRACTION100

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