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- PDB-5fb2: S. aureus MepR F27L Mutant bound to oligodeoxyribonucleotide -

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Basic information

Entry
Database: PDB / ID: 5fb2
TitleS. aureus MepR F27L Mutant bound to oligodeoxyribonucleotide
Components
  • DNA (5'-D(*CP*GP*TP*TP*A)-3')
  • MarR family regulatory protein
KeywordsTRANSCRIPTION/DNA / Winged helix-turn-helix / protein-ligand complex / transcription regulation / multidrug resistance / single-stranded DNA / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


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
DNA / MarR family regulatory protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBirukou, I. / Newman, C.E. / Brennan, R.G.
CitationJournal: To Be Published
Title: S. aureus MepR F27L Mutant bound to oligodeoxyribonucleotide
Authors: Birukou, I. / Newman, C.E. / Brennan, R.G.
History
DepositionDec 13, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 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
B: DNA (5'-D(*CP*GP*TP*TP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8153
Polymers17,7232
Non-polymers921
Water2,306128
1
A: MarR family regulatory protein
B: DNA (5'-D(*CP*GP*TP*TP*A)-3')
hetero molecules

A: MarR family regulatory protein
B: DNA (5'-D(*CP*GP*TP*TP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6316
Polymers35,4474
Non-polymers1842
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Unit cell
Length a, b, c (Å)32.263, 97.986, 106.317
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-367-

HOH

21A-418-

HOH

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Components

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


Mass: 16228.272 Da / Num. of mol.: 1 / Mutation: F27L
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: DNA chain DNA (5'-D(*CP*GP*TP*TP*A)-3')


Mass: 1495.023 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.37 Å3/Da / Density % sol: 48.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 20% (w/v) Peg 1000, 100 mM Potassium phosphate monobasic/Sodium phosphate dibasic buffer, 200 mM Sodium chloride

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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 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→36.03 Å / Num. obs: 15799 / % possible obs: 98.1 % / Redundancy: 2.81 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 10.5

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
d*TREKdata reduction
d*TREKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ECO

3eco


Resolution: 1.8→36.026 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2318 1579 10 %
Rwork0.1876 --
obs0.1921 15794 98.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→36.026 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1103 98 6 128 1335
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071285
X-RAY DIFFRACTIONf_angle_d0.9451761
X-RAY DIFFRACTIONf_dihedral_angle_d16.782506
X-RAY DIFFRACTIONf_chiral_restr0.057201
X-RAY DIFFRACTIONf_plane_restr0.004214
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8001-1.85820.32551360.32341225X-RAY DIFFRACTION95
1.8582-1.92460.34031440.30271294X-RAY DIFFRACTION100
1.9246-2.00160.34491440.25951300X-RAY DIFFRACTION100
2.0016-2.09270.27031430.23631279X-RAY DIFFRACTION100
2.0927-2.2030.2421420.21651284X-RAY DIFFRACTION99
2.203-2.3410.27841440.2071300X-RAY DIFFRACTION98
2.341-2.52170.25731430.20641280X-RAY DIFFRACTION98
2.5217-2.77540.23241420.20311282X-RAY DIFFRACTION98
2.7754-3.17680.19581450.18461306X-RAY DIFFRACTION98
3.1768-4.00160.26791470.16241321X-RAY DIFFRACTION98
4.0016-36.03320.18081490.16461344X-RAY DIFFRACTION95
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.24960.0794-0.5782.3663-1.97852.0520.0321-0.0256-0.13440.1921-0.17090.0034-0.05980.14940.25150.2439-0.0095-0.00080.2336-0.01870.22011.2038-33.967516.6288
22.118-1.4583-0.01263.33180.17713.3778-0.1518-0.20330.20260.3530.0917-0.0586-0.35360.09260.0790.2525-0.0138-0.01330.2301-0.020.2343-6.5495-15.44927.4478
3-0.1535-0.32410.5382.235-1.92961.7090.0468-0.0380.0046-0.2994-0.07940.09110.32640.02520.01260.2908-0.01590.03250.2724-0.02640.2589-3.0215-47.210316.7667
43.1942.70682.69475.2979-1.51127.90550.0902-1.0456-0.05241.38430.04580.59470.4422-0.0884-0.0620.5560.02490.14370.3940.04920.4869-6.936-32.978716.4915
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 49 )
2X-RAY DIFFRACTION2chain 'A' and (resid 50 through 94 )
3X-RAY DIFFRACTION3chain 'A' and (resid 95 through 139 )
4X-RAY DIFFRACTION4chain 'B' and (resid 4 through 8 )

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