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- PDB-5ffx: S. aureus MepR G34K Mutant -

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Basic information

Entry
Database: PDB / ID: 5ffx
TitleS. aureus MepR G34K Mutant
ComponentsMarR family regulatory protein
KeywordsTRANSCRIPTION REGULATOR / Winged helix-turn-helix / DNA binding protein / transcription regulation / multidrug resistance
Function / homology
Function and homology information


response to stress / DNA-binding transcription factor activity / regulation of DNA-templated transcription
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
HTH marR-type domain-containing protein / MarR family regulatory protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsNewman, C.E. / Birukou, I. / Brennan, R.G.
CitationJournal: To Be Published
Title: S. aureus MepR G34K Mutant
Authors: Newman, C.E. / Birukou, I. / 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
D: MarR family regulatory protein
B: MarR family regulatory protein
C: MarR family regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,65719
Polymers75,2244
Non-polymers1,43315
Water14,646813
1
A: MarR family regulatory protein
B: MarR family regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2859
Polymers37,6122
Non-polymers6727
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4860 Å2
ΔGint-117 kcal/mol
Surface area15960 Å2
MethodPISA
2
D: MarR family regulatory protein
C: MarR family regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,37310
Polymers37,6122
Non-polymers7618
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-101 kcal/mol
Surface area16200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.297, 96.461, 109.486
Angle α, β, γ (deg.)90.00, 90.66, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 18806.090 Da / Num. of mol.: 4 / Mutation: G34K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: mepR / Plasmid: PMCSG7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5Y812, UniProt: Q2G141*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 813 / 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: 2.27 Å3/Da / Density % sol: 45.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 800mM ammonium sulfate, 100 mM citric acid/sodium hydroxide pH 4.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jul 31, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.47→30.62 Å / Num. obs: 112058 / % possible obs: 98.29 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.084 / Rsym value: 0.07 / Net I/σ(I): 13.45
Reflection shellResolution: 1.48→1.51 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.675 / Mean I/σ(I) obs: 2.8 / % possible all: 92.58

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Processing

Software
NameVersionClassification
PHENIX1.7.1_743refinement
Cootmodel building
HKL-3000data scaling
PHENIXphasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4L9T

4l9t


Resolution: 1.47→30.62 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1924 1994 1.78 %
Rwork0.1537 --
obs0.1544 112044 98.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.392 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.5264 Å20 Å20.5206 Å2
2--2.4206 Å20 Å2
3----2.947 Å2
Refinement stepCycle: LAST / Resolution: 1.47→30.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4443 0 77 813 5333
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095092
X-RAY DIFFRACTIONf_angle_d1.0916918
X-RAY DIFFRACTIONf_dihedral_angle_d13.6031989
X-RAY DIFFRACTIONf_chiral_restr0.073758
X-RAY DIFFRACTIONf_plane_restr0.005909
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4684-1.50510.28641300.22077101X-RAY DIFFRACTION90
1.5051-1.54580.24251390.19937946X-RAY DIFFRACTION99
1.5458-1.59130.21411410.16397933X-RAY DIFFRACTION100
1.5913-1.64260.24371430.15117960X-RAY DIFFRACTION100
1.6426-1.70140.17831470.14388034X-RAY DIFFRACTION100
1.7014-1.76950.20481430.13287873X-RAY DIFFRACTION100
1.7695-1.850.18031470.13037992X-RAY DIFFRACTION100
1.85-1.94750.16971420.12167917X-RAY DIFFRACTION100
1.9475-2.06950.16561500.12727982X-RAY DIFFRACTION99
2.0695-2.22920.18581480.12767919X-RAY DIFFRACTION99
2.2292-2.45350.16341400.1397985X-RAY DIFFRACTION99
2.4535-2.80830.17821440.14887978X-RAY DIFFRACTION99
2.8083-3.53730.18911470.14958000X-RAY DIFFRACTION99
3.5373-30.63080.21491330.18757430X-RAY DIFFRACTION91

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