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- PDB-9zpj: Crystal structure of MrtR bound to 3OH-C8 homoserine lactone -

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Basic information

Entry
Database: PDB / ID: 9zpj
TitleCrystal structure of MrtR bound to 3OH-C8 homoserine lactone
ComponentsMrtR
KeywordsTRANSCRIPTION / quorum sensing receptor
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Transcription factor LuxR-like, autoinducer-binding domain / Transcription factor LuxR-like, autoinducer-binding domain superfamily / Autoinducer binding domain / LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / Signal transduction response regulator, C-terminal effector / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
: / DI(HYDROXYETHYL)ETHER / MrtR
Similarity search - Component
Biological speciesMesorhizobium tianshanense (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.176 Å
AuthorsStoutland, I.M. / Bingman, C.A. / Blackwell, H.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)2R35GM131817-06 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2026
Title: MrtR of Mesorhizobium tianshanense reveals both activation and inhibition mechanisms of a LuxR-type quorum sensing receptor.
Authors: Stoutland, I.M. / Blackwell, H.E.
History
DepositionDec 16, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MrtR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,37511
Polymers27,2761
Non-polymers1,09810
Water5,062281
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)125.315, 35.552, 61.649
Angle α, β, γ (deg.)90.000, 111.658, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-633-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein MrtR


Mass: 27276.066 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesorhizobium tianshanense (bacteria) / Gene: mrtR / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q45NF4

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Non-polymers , 5 types, 291 molecules

#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-A1C3P / (3R)-3-hydroxy-N-[(3S)-2-oxooxolan-3-yl]octanamide / N-3-hydroxyoctanoyl-L-Homoserine lactone


Mass: 243.299 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H21NO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.34 Å3/Da / Density % sol: 47.43 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: imidazole, MES, diethylene glycol, triethylene glycol, tetraethylene glycol, pentaethylene glycol, 2-Methyl-2,4-pentanediol (MPD), PEG 1000, PEG 3350, N-3-hydroxyoctanoyl-L-Homoserine ...Details: imidazole, MES, diethylene glycol, triethylene glycol, tetraethylene glycol, pentaethylene glycol, 2-Methyl-2,4-pentanediol (MPD), PEG 1000, PEG 3350, N-3-hydroxyoctanoyl-L-Homoserine lactone, DMSO. 2:1 protein:buffer

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM07 / Wavelength: 0.980114 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 19, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980114 Å / Relative weight: 1
ReflectionResolution: 1.176→51 Å / Num. obs: 77750 / % possible obs: 92.4 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.04 / Net I/σ(I): 13.5
Reflection shellResolution: 1.176→1.197 Å / Redundancy: 6.3 % / Num. unique obs: 4011 / CC1/2: 0.385 / % possible all: 96.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.176→51 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.977 / SU B: 1.818 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.041 / ESU R Free: 0.04
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.1731 3872 4.991 %RANDOM
Rwork0.1461 73709 --
all0.147 ---
obs-77581 92.129 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 21.406 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å2-0 Å20.009 Å2
2--0.605 Å2-0 Å2
3----0.328 Å2
Refinement stepCycle: LAST / Resolution: 1.176→51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1918 0 69 281 2268
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0122384
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162305
X-RAY DIFFRACTIONr_angle_refined_deg1.6591.8273258
X-RAY DIFFRACTIONr_angle_other_deg0.6191.825313
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1375308
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.611522
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.35410401
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.99810112
X-RAY DIFFRACTIONr_chiral_restr0.0930.2350
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022919
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02575
X-RAY DIFFRACTIONr_nbd_refined0.2570.2480
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1980.21858
X-RAY DIFFRACTIONr_nbtor_refined0.1850.21016
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.21065
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2178
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.170.29
X-RAY DIFFRACTIONr_nbd_other0.1520.241
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1180.227
X-RAY DIFFRACTIONr_mcbond_it5.772.0371133
X-RAY DIFFRACTIONr_mcbond_other5.7462.0371133
X-RAY DIFFRACTIONr_mcangle_it8.2343.6671446
X-RAY DIFFRACTIONr_mcangle_other8.2343.6681447
X-RAY DIFFRACTIONr_scbond_it7.4212.4081251
X-RAY DIFFRACTIONr_scbond_other7.4182.4091252
X-RAY DIFFRACTIONr_scangle_it10.2074.2471801
X-RAY DIFFRACTIONr_scangle_other10.2044.2471802
X-RAY DIFFRACTIONr_lrange_it15.7323.3292675
X-RAY DIFFRACTIONr_lrange_other15.72823.332676
X-RAY DIFFRACTIONr_rigid_bond_restr3.66834689
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.176-1.2070.3262830.3235681X-RAY DIFFRACTION95.9459
1.207-1.240.3312550.3134736X-RAY DIFFRACTION83.4058
1.24-1.2760.2882580.2915079X-RAY DIFFRACTION90.7344
1.276-1.3150.2732560.2574947X-RAY DIFFRACTION91.2647
1.315-1.3580.2212850.2045188X-RAY DIFFRACTION99.1126
1.358-1.4060.2272540.1954540X-RAY DIFFRACTION90.1297
1.406-1.4590.1952110.1654560X-RAY DIFFRACTION92.7488
1.459-1.5180.1792650.1454319X-RAY DIFFRACTION91.7534
1.518-1.5860.1582240.1144108X-RAY DIFFRACTION90.6656
1.586-1.6630.152280.1054285X-RAY DIFFRACTION99.0779
1.663-1.7530.1622100.1053909X-RAY DIFFRACTION94.6027
1.753-1.8590.1532090.1123833X-RAY DIFFRACTION98.1306
1.859-1.9870.1631430.1142812X-RAY DIFFRACTION76.1794
1.987-2.1460.1631610.1193073X-RAY DIFFRACTION89.659
2.146-2.3510.1621710.1182917X-RAY DIFFRACTION92.5659
2.351-2.6270.1681430.1232815X-RAY DIFFRACTION98.5343
2.627-3.0330.166960.142328X-RAY DIFFRACTION90.3466
3.033-3.7110.1721070.1371982X-RAY DIFFRACTION91.905
3.711-5.2350.144810.1411596X-RAY DIFFRACTION93.3222
5.235-510.172330.2041001X-RAY DIFFRACTION99.6146

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