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- PDB-9smz: Structure of Staphylococcus aureus MarR-type repressor MhqR bound... -

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Basic information

Entry
Database: PDB / ID: 9smz
TitleStructure of Staphylococcus aureus MarR-type repressor MhqR bound to MBQ
ComponentsMarR family transcriptional regulator
KeywordsDNA BINDING PROTEIN / MarR-type Repressor / Winged Helix-Turn-Helix / Dimer
Function / homology
Function and homology information


DNA-binding transcription factor activity
Similarity search - Function
Transcriptional regulator MarR-type, conserved site / MarR-type HTH domain signature. / MarR family / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
: / MarR family transcriptional regulator
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsWeiland, P. / Kiontke, S. / Bange, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Mbio / Year: 2025
Title: Structural basis of quinone sensing by the MarR-type repressor MhqR in Staphylococcus aureus.
Authors: Nguyen, T.T.-.P. / Weiland, P. / Loi, V.V. / Kiontke, S. / Burchert, F. / Zegarra, V. / Kern, A. / Fritsch, V.N. / Baranov, D. / Bronowska, A.K. / Bange, G. / Antelmann, H.
History
DepositionSep 9, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 14, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MarR family transcriptional regulator
B: MarR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6815
Polymers35,3142
Non-polymers3663
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Dimerization was validated by analytical SEC coupled to multi angle light scattering (SEC-MALS)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5950 Å2
ΔGint-48 kcal/mol
Surface area15000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.340, 73.640, 95.160
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid 0 through 148)
d_2ens_1(chain "B" and resid 0 through 148)

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: HIS / End label comp-ID: HIS / Auth seq-ID: 0 - 148 / Label seq-ID: 3 - 151

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB

NCS oper: (Code: givenMatrix: (-0.99999886866, 0.00107928353159, 0.00104777211596), (-0.0010829493349, -0.999993273092, -0.0035044245905), (0.00104398279995, -0.00350555530992, 0.999993310569)Vector: ...NCS oper: (Code: given
Matrix: (-0.99999886866, 0.00107928353159, 0.00104777211596), (-0.0010829493349, -0.999993273092, -0.0035044245905), (0.00104398279995, -0.00350555530992, 0.999993310569)
Vector: 70.9467209059, 101.005437706, 0.19116241332)

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Components

#1: Protein MarR family transcriptional regulator / Transcriptional regulator / MarR family


Mass: 17657.215 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: ACR74_11585, CNH36_14130, CV021_15190, DQU50_12220, DQV00_06695, E1948_07105, E1948_13375, EIH03_11480, EP54_00620, EQ90_03220, ERS1058648_02219, ERS329596_00428, G0Z31_03645, G6Y24_16615, ...Gene: ACR74_11585, CNH36_14130, CV021_15190, DQU50_12220, DQV00_06695, E1948_07105, E1948_13375, EIH03_11480, EP54_00620, EQ90_03220, ERS1058648_02219, ERS329596_00428, G0Z31_03645, G6Y24_16615, GO814_08825, GO942_11125, GQX37_12890, GQX52_00115, GZ164_11830, LB359_10620, M1K003_1959, NCTC10702_03913, NCTC13131_00022, NCTC5664_01261, NCTC6133_03383, NCTC7878_03598, NCTC7972_02126, QU38_16550, SAMEA1029528_00885, SAMEA1029536_01144, SAMEA1466929_02220, SAMEA1531725_00431, SAMEA2078260_01128, SAMEA2078588_01170, SAMEA2080344_00642, SAMEA2081063_00938, SAMEA4008575_00765, SAMEA4552975_01915, SAMEA70146418_00214, SAMEA70153168_01173, SAMEA70245418_00263
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: W8U802
#2: Chemical ChemComp-YMR / 2-methylcyclohexa-2,5-diene-1,4-dione


Mass: 122.121 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.35 Å3/Da / Density % sol: 47.63 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 2 mM of protein was mixed with 10 mM 2-Methylhydroquinone in 20 mM HEPES pH 7.5, 200 mM NaCl and 20 mM KCl and mixed with 1.0-1.2 M tri-Sodium citrate 0.1 M Sodium HEPES pH 7.5 in a 1:1 and 1:2 ratio.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.967697 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: May 18, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.967697 Å / Relative weight: 1
ReflectionResolution: 2.28→47.58 Å / Num. obs: 15743 / % possible obs: 99.9 % / Redundancy: 12.37 % / Biso Wilson estimate: 31.87 Å2 / CC1/2: 0.994 / Rrim(I) all: 0.239 / Net I/σ(I): 7.9
Reflection shellResolution: 2.28→2.42 Å / Mean I/σ(I) obs: 2.68 / Num. unique obs: 2484 / CC1/2: 0.918 / Rrim(I) all: 0.827 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.28→47.58 Å / SU ML: 0.318 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 33.7522
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2828 788 5.01 %
Rwork0.2398 14941 -
obs0.242 15729 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.16 Å2
Refinement stepCycle: LAST / Resolution: 2.28→47.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2318 0 27 79 2424
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00822406
X-RAY DIFFRACTIONf_angle_d0.97653238
X-RAY DIFFRACTIONf_chiral_restr0.051368
X-RAY DIFFRACTIONf_plane_restr0.008424
X-RAY DIFFRACTIONf_dihedral_angle_d19.192928
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.770407317211 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.28-2.420.34861290.27252432X-RAY DIFFRACTION99.81
2.42-2.610.32721280.25352449X-RAY DIFFRACTION99.88
2.61-2.870.321300.25062459X-RAY DIFFRACTION99.85
2.87-3.290.30341300.24142460X-RAY DIFFRACTION99.88
3.29-4.140.21651320.21632517X-RAY DIFFRACTION99.77
4.14-47.580.28411390.23922624X-RAY DIFFRACTION99.82

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