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- PDB-9qdr: Structure of Staphylococcus aureus MarR-type repressor MhqR -

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Basic information

Entry
Database: PDB / ID: 9qdr
TitleStructure of Staphylococcus aureus MarR-type repressor MhqR
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
TRIETHYLENE GLYCOL / MarR family transcriptional regulator
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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
DepositionMar 6, 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)35,6154
Polymers35,3142
Non-polymers3002
Water3,531196
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, As provided in the publication text we performed size exclusion chromatography coupled multi-angle light scattering experiments to support the formation of a MhqR dimer in solution.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6060 Å2
ΔGint-35 kcal/mol
Surface area15930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.920, 69.430, 71.650
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

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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 (E. coli) / References: UniProt: W8U802
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C6H14O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 1.83 Å3/Da / Density % sol: 32.73 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 0.1 M phosphate-citrate pH 4.0 30% PEG 300

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97626 Å
DetectorType: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Jun 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 1.55→49.86 Å / Num. obs: 38191 / % possible obs: 99.75 % / Redundancy: 13 % / Biso Wilson estimate: 18.23 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.1332 / Rpim(I) all: 0.03828 / Rrim(I) all: 0.1387 / Net I/σ(I): 11.04
Reflection shellResolution: 1.55→1.59 Å / Redundancy: 12.2 % / Mean I/σ(I) obs: 1.79 / Num. unique obs: 2589 / CC1/2: 0.612 / % possible all: 96.68

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→49.86 Å / SU ML: 0.1887 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.8301
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2229 1909 5 %
Rwork0.1847 36278 -
obs0.1866 38187 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.08 Å2
Refinement stepCycle: LAST / Resolution: 1.55→49.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2328 0 20 196 2544
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01472387
X-RAY DIFFRACTIONf_angle_d1.32613204
X-RAY DIFFRACTIONf_chiral_restr0.0796370
X-RAY DIFFRACTIONf_plane_restr0.0106405
X-RAY DIFFRACTIONf_dihedral_angle_d18.2296919
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.590.28231300.25612459X-RAY DIFFRACTION96.68
1.59-1.630.27511350.22452575X-RAY DIFFRACTION100
1.63-1.680.28251350.22662550X-RAY DIFFRACTION100
1.68-1.730.27171360.21742582X-RAY DIFFRACTION100
1.73-1.80.27341340.2232539X-RAY DIFFRACTION99.96
1.8-1.870.26061350.20182580X-RAY DIFFRACTION100
1.87-1.950.28571350.18722565X-RAY DIFFRACTION100
1.95-2.060.20641370.18152585X-RAY DIFFRACTION100
2.06-2.180.21341360.17922587X-RAY DIFFRACTION100
2.18-2.350.20981360.17182590X-RAY DIFFRACTION100
2.35-2.590.21191370.18482602X-RAY DIFFRACTION100
2.59-2.970.23871380.18382624X-RAY DIFFRACTION99.93
2.97-3.730.21551390.17092664X-RAY DIFFRACTION100
3.74-49.860.19091460.17522776X-RAY DIFFRACTION99.93
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)
1-0.001143168723130.160603005979-0.04046807016520.2953177712280.2000265972370.2988034770220.03730316364720.0690481665370.006221758709040.0900460534001-0.0858401569595-0.0581498562393-0.0178732981166-0.0544037949490.0001145600406280.1243042233190.00752327528696-0.008259500286820.135298611033-0.0009583502243770.12279601961615.1293087342-1.481313304755.01098967764
21.030650800010.04576606658140.6043778960150.75073314511-0.006090276997531.149427358520.01078787089530.1198472358620.258003822389-0.139329136602-0.0491058604343-0.0500957844035-0.1256459857320.289840845956-0.00527361741410.150089281260.001318787685050.02148058351550.1752569507730.03007288697960.16620961726127.2223722793-11.704629345-17.3641851063
30.4995558085970.2894536422340.0805253348016-0.839120246828-0.1981153072641.08293883319-0.0506634529314-0.03369802318850.0671344068642-0.111309524994-0.07411439720210.137518479333-0.351568324293-0.0632665026745-0.08468363743380.2303859625710.0182518548192-0.04382547537270.0825688667524-0.04277045355550.137137707569.03228806744-6.75750252559-9.98163514985
40.1002351734590.0776010209403-0.05760138118740.42151182932-0.1574691559520.6034458477170.03785173941290.1221483997480.0017393890679-0.005597229704430.02798994588680.0294960933776-0.1315578557340.03724713695240.04154420258660.15684129106-0.02769292543930.01168839193390.1215117560830.02524257342130.12329987750916.6708213220.217403931274-3.76997984264
50.1974097435770.07608263192630.1152298937530.1494974616260.04629960405810.319197760071-0.04736824324930.2462197468170.0818655091459-0.07425316856840.0871182801360.0323778441879-0.141551582365-0.1533393609290.005555174772110.133884087965-0.0254410795687-0.002564586542510.1475498115850.008994715997240.14473910029327.29860587757.4936399101512.0603180397
60.05786446819970.06571276832380.07561355751580.06428777316840.0734750355440.209523299393-0.0648352964586-0.103078590993-0.3053793683690.439752462485-0.1617898231320.2612037936820.68790538165-0.230132764358-0.007260335389750.296208699246-0.03857235783630.007947193790260.1494538071770.004946591784430.25274088462425.7884446236-1.60466113319.2207780238
70.05816177389710.198676134437-0.134224698440.471424155578-0.4020857563610.512019007747-0.01861914986660.609523978192-0.490958857979-0.05811185842460.301875613104-0.192882841190.08232974615270.1916199684840.06432795018590.1597790986920.001710104009840.001048773466580.228221683934-0.08363887703040.27308906764834.11842049261.303195005811.4767673068
80.123059622842-0.0792850461528-0.05860104532750.268052771292-0.028996504990.0777654506868-0.02091718142420.172228224359-0.2812397149050.2140765875510.000700098945148-0.1692612498470.2419561870570.4579240703720.00284386722710.193799159990.0246712574559-0.03508300529930.2036672942620.02526219548770.23909264264836.38679638115.215155750820.6124467217
91.1643296068-0.404608115839-0.08559653265850.4636109620110.5612755626430.9355136075340.1773730716860.1218022894130.198899568023-0.157851725803-0.0895328247075-0.122196061877-0.0727987584550.09611983945950.3897088578240.1678196391490.01791491656240.03333128477720.1390615316970.04233913564840.16058965607224.957569593914.361211914111.6044033563
100.5604555196750.5687237325920.1949151061840.7370927953280.7003095613510.8391192981340.141843651826-0.1074349719460.0180362279895-0.111412626286-0.3150545213170.313105927045-0.0148894336221-0.169651921168-0.0693770489660.1529736360130.0334839378232-0.01577354938050.155462394425-0.03304996991150.1476962288057.71851263152-0.8229773441344.85934906393
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid -1 through 31 )AA-1 - 311 - 33
22chain 'A' and (resid 32 through 97 )AA32 - 9734 - 98
33chain 'A' and (resid 98 through 150 )AA98 - 15099 - 151
44chain 'B' and (resid -1 through 32 )BC-1 - 321 - 34
55chain 'B' and (resid 33 through 48 )BC33 - 4835 - 50
66chain 'B' and (resid 49 through 59 )BC49 - 5951 - 61
77chain 'B' and (resid 60 through 76 )BC60 - 7662 - 78
88chain 'B' and (resid 77 through 92 )BC77 - 9279 - 87
99chain 'B' and (resid 93 through 119 )BC93 - 11988 - 114
1010chain 'B' and (resid 120 through 145 )BC120 - 145115 - 140

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