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- PDB-4l9j: Crystal structure of S. aureus MepR in DNA-binding conformation -

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Basic information

Entry
Database: PDB / ID: 4l9j
TitleCrystal structure of S. aureus MepR in DNA-binding conformation
ComponentsMepR
KeywordsTRANSCRIPTION / winged helix-turn-helix / wHTH / transcription repressor
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
MarR family regulatory protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.45 Å
AuthorsBirukou, I. / Brennan, R.G.
CitationJournal: MBio / Year: 2013
Title: The molecular mechanisms of allosteric mutations impairing MepR repressor function in multidrug-resistant strains of Staphylococcus aureus.
Authors: Birukou, I. / Tonthat, N.K. / Seo, S.M. / Schindler, B.D. / Kaatz, G.W. / Brennan, R.G.
History
DepositionJun 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MepR
B: MepR


Theoretical massNumber of molelcules
Total (without water)32,9942
Polymers32,9942
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint-35 kcal/mol
Surface area14520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.806, 98.806, 151.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein MepR / MarR family transcription repressor MepR


Mass: 16496.762 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: NCTC 8325-4 / Gene: mepR / Production host: Escherichia coli (E. coli) / Strain (production host): C41 / References: UniProt: Q5Y812

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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: 5.6 Å3/Da / Density % sol: 78.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 2 mM CuCl2, 50 mM Tris HCl pH 8.5, 1.8 M Li2SO4, and 0.5 mM spermine, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.97236 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 11, 2012
RadiationMonochromator: Rosenbaum-Rock double-crystal monochromator: liquid nitrogen cooled, sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97236 Å / Relative weight: 1
ReflectionResolution: 3.45→50 Å / Num. all: 10396 / Num. obs: 10448 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2.13

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Processing

Software
NameVersionClassification
SERGUIcontrol programdata collection
PHENIX(Phaser)model building
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX(Phaser)phasing
RefinementMethod to determine structure: SAD / Resolution: 3.45→34.04 Å / SU ML: 0.38 / σ(F): 0 / Phase error: 27.42 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2643 1014 9.99 %random
Rwork0.2248 ---
obs0.2288 10153 97.59 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.45→34.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2180 0 0 0 2180
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122218
X-RAY DIFFRACTIONf_angle_d1.6492988
X-RAY DIFFRACTIONf_dihedral_angle_d17.93832
X-RAY DIFFRACTIONf_chiral_restr0.082343
X-RAY DIFFRACTIONf_plane_restr0.009386
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.45-3.63190.33651310.28351176X-RAY DIFFRACTION90
3.6319-3.85920.32941380.2481271X-RAY DIFFRACTION97
3.8592-4.15670.26161430.20011276X-RAY DIFFRACTION98
4.1567-4.57410.20151460.16951313X-RAY DIFFRACTION99
4.5741-5.23390.23811470.1791330X-RAY DIFFRACTION99
5.2339-6.58640.29571500.28091352X-RAY DIFFRACTION100
6.5864-34.040.26351590.23571421X-RAY DIFFRACTION99
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)
1-0.02330.003-0.09920.5973-0.52540.44980.2616-0.0429-0.13220.46120.1115-0.5220.03510.07110.85470.4128-0.2192-0.34150.38310.14540.368628.284681.270212.3292
20.160.1365-0.18550.2386-0.05960.2354-0.2283-0.39260.5328-0.16940.00610.17880.2299-0.8714-0.02890.2366-0.0268-0.06720.75110.06590.44717.702493.15485.7083
30.4787-0.03970.47540.0192-0.08160.5726-0.05610.1740.2258-0.0501-0.2202-0.2625-0.12190.0759-0.54160.22530.5358-0.43280.75160.73630.69275.1695.83256.2165
40.7910.0165-0.42410.5451-0.28080.3231-0.0319-1.4828-0.15790.8537-0.2098-0.2038-0.0561-0.3963-0.09020.4362-0.14570.0620.71570.120.435615.7254101.133510.9594
51.51450.99770.78410.9191-0.11761.82890.48310.1949-1.1399-0.05520.35780.16250.94430.01922.33560.64440.0049-0.20450.21790.18110.445514.283492.07632.226
61.7902-1.11040.53910.9198-0.45350.2038-0.4562-0.74640.46440.60090.4567-0.1545-0.1345-0.3704-0.20280.22720.2754-0.0379-0.18840.24871.022813.49572.064114.4693
71.85140.2766-0.8260.0614-0.07680.44010.10610.76170.00330.31970.49430.6536-0.7277-0.18960.22350.99140.1939-0.15760.52530.0290.606521.913784.804222.8806
82.02360.54081.48090.6793-0.542.6425-0.576-0.44430.7638-0.0634-0.29730.1848-0.0833-0.0777-2.04230.56310.09050.14760.2028-0.1033-0.237137.532575.089329.486
94.3876-1.31451.34290.4041-0.36260.512-0.61350.13850.9359-0.6655-0.0457-0.6153-0.75340.2793-0.26111.0965-0.2563-0.04760.50550.13890.43442.332483.333622.9776
100.87420.9184-0.01882.055-1.3651.6242-0.45680.33820.1425-0.2706-0.4642-0.33230.4309-0.0272-1.86550.2635-0.01820.02460.5846-0.07610.18749.580377.191929.9054
110.51170.689-0.01121.4150.5950.63860.0261-0.00240.1460.3310.15441.0555-0.7355-0.55740.42640.5470.0878-0.10280.43350.07380.41626.597377.122734.4745
120.966-0.25220.52950.2197-0.06830.32780.73530.6982-0.334-1.03550.1518-0.21010.74170.27840.180.93790.1343-0.23240.4106-0.10050.757621.198767.800616.3444
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 27 )
2X-RAY DIFFRACTION2chain 'A' and (resid 28 through 43 )
3X-RAY DIFFRACTION3chain 'A' and (resid 44 through 49 )
4X-RAY DIFFRACTION4chain 'A' and (resid 50 through 80 )
5X-RAY DIFFRACTION5chain 'A' and (resid 81 through 117 )
6X-RAY DIFFRACTION6chain 'A' and (resid 118 through 139 )
7X-RAY DIFFRACTION7chain 'B' and (resid 3 through 30 )
8X-RAY DIFFRACTION8chain 'B' and (resid 31 through 49 )
9X-RAY DIFFRACTION9chain 'B' and (resid 50 through 73 )
10X-RAY DIFFRACTION10chain 'B' and (resid 74 through 94 )
11X-RAY DIFFRACTION11chain 'B' and (resid 95 through 117 )
12X-RAY DIFFRACTION12chain 'B' and (resid 118 through 139 )

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