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- PDB-5f6f: S. aureus MepR G34R Mutant -

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Basic information

Entry
Database: PDB / ID: 5f6f
TitleS. aureus MepR G34R 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: 1.751 Å
AuthorsNewman, C.E. / Birukou, I. / Brennan, R.G.
CitationJournal: To Be Published
Title: S. aureus MepR G34R Mutant
Authors: Newman, C.E. / Birukou, I. / Brennan, R.G.
History
DepositionDec 5, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 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: MarR family regulatory protein


Theoretical massNumber of molelcules
Total (without water)37,6682
Polymers37,6682
Non-polymers00
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-36 kcal/mol
Surface area16900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.949, 119.949, 55.798
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

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


Mass: 18834.104 Da / Num. of mol.: 2 / Mutation: G34R
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) / References: UniProt: Q5Y812, UniProt: Q2G141*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.19 Å3/Da / Density % sol: 43.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 25% (w/v) Peg 1500, 100 mM MIB buffer (Imidazole, Boric Acid, Sodium Malonate Dibasic Monohydrate)

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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: 1.75→29.99 Å / Num. obs: 29854 / % possible obs: 99.1 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.08 / Rsym value: 0.071 / Net I/σ(I): 14.1
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.825 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.7.1_743refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FFZ

5ffz


Resolution: 1.751→29.987 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 23.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.226 1997 6.69 %
Rwork0.1872 --
obs0.1899 29846 99.12 %
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.883 Å2 / ksol: 0.433 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.3334 Å20 Å2-0 Å2
2---2.3334 Å20 Å2
3---4.6668 Å2
Refinement stepCycle: LAST / Resolution: 1.751→29.987 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2282 0 0 138 2420
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062561
X-RAY DIFFRACTIONf_angle_d0.9663486
X-RAY DIFFRACTIONf_dihedral_angle_d13.3421001
X-RAY DIFFRACTIONf_chiral_restr0.069385
X-RAY DIFFRACTIONf_plane_restr0.004464
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7513-1.79510.39561440.32822000X-RAY DIFFRACTION100
1.7951-1.84360.36311460.27832014X-RAY DIFFRACTION100
1.8436-1.89790.24081410.22741963X-RAY DIFFRACTION100
1.8979-1.95910.25951420.20952033X-RAY DIFFRACTION100
1.9591-2.02910.26491400.2211997X-RAY DIFFRACTION100
2.0291-2.11030.25791460.21242027X-RAY DIFFRACTION100
2.1103-2.20630.20461440.20171990X-RAY DIFFRACTION100
2.2063-2.32260.2411460.19432027X-RAY DIFFRACTION100
2.3226-2.46810.2191450.21372002X-RAY DIFFRACTION100
2.4681-2.65850.23881420.19762014X-RAY DIFFRACTION100
2.6585-2.92590.26651470.19592009X-RAY DIFFRACTION100
2.9259-3.34880.22731410.18542002X-RAY DIFFRACTION100
3.3488-4.21720.17791410.15452014X-RAY DIFFRACTION100
4.2172-29.99160.23141320.18431757X-RAY DIFFRACTION88
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)
15.45625.3166-3.1644.734-4.18296.10480.1811-0.5258-1.01720.3111-0.4636-1.29730.26060.36150.32550.3043-0.0455-0.14150.3630.04060.483734.003614.174-21.8589
22.733-1.246-0.29599.0255-3.97757.42280.34450.3486-0.2065-0.1414-0.2746-0.1876-0.20050.3633-0.06770.3814-0.05450.00010.2277-0.04240.362716.463-5.1472-23.3395
38.48031.5016-2.13184.67573.6157.42490.41860.5671-0.1538-0.39750.2398-0.153-0.22610.2072-0.62530.40030.00710.07080.2316-0.0080.432816.0351-13.7827-28.8977
42.25342.9394-0.13668.6571-0.73050.15960.1974-0.0722-0.13030.7525-0.12270.04090.04790.0858-0.04090.3753-0.0050.07550.2817-0.02970.184410.8914-4.2742-19.29
54.4183-3.0799-4.00617.301-0.72149.44040.19180.6759-0.1189-0.1273-0.19020.2632-0.4895-0.45610.01160.3102-0.04-0.06040.3976-0.03910.340922.076822.6101-30.8164
63.82641.0774-3.91151.04260.20385.9127-0.31720.3188-1.2457-0.21160.1151-0.20380.3950.14530.29170.2931-0.0542-0.03650.3468-0.11120.469731.097312.3463-33.7121
77.78750.2259-1.00627.1753-0.98948.32390.03610.1428-0.10050.42390.2003-0.13640.0141-0.3374-0.19660.19240.0448-0.010.40260.00960.344656.334218.4399-32.1716
86.87740.22431.33018.321-1.10113.43320.5271-0.3206-0.25080.73020.1892-0.1835-0.0931-0.3662-0.74440.31160.0570.02980.37550.08870.444663.343713.789-26.5642
95.0891-1.5122-1.62070.44560.1561-0.07170.13920.97160.1762-0.0791-0.1849-0.05920.07440.00630.07560.31880.0406-0.0050.42950.06910.260458.013822.5778-36.6706
107.59672.0065-2.84529.929-5.02919.44990.09120.11970.52490.7497-0.2306-0.1524-0.8084-0.16440.14810.322-0.0204-0.05830.3531-0.05980.346729.600526.8197-25.2098
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq -1:26)
2X-RAY DIFFRACTION2chain 'A' and (resseq 27:46)
3X-RAY DIFFRACTION3chain 'A' and (resseq 47:73)
4X-RAY DIFFRACTION4chain 'A' and (resseq 74:118)
5X-RAY DIFFRACTION5chain 'A' and (resseq 119:139)
6X-RAY DIFFRACTION6chain 'B' and (resseq -1:26)
7X-RAY DIFFRACTION7chain 'B' and (resseq 27:46)
8X-RAY DIFFRACTION8chain 'B' and (resseq 47:73)
9X-RAY DIFFRACTION9chain 'B' and (resseq 74:118)
10X-RAY DIFFRACTION10chain 'B' and (resseq 119:139)

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