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- PDB-9y2h: Crystal structure of MrtR bound to 7Z-3OH-C14 homoserine lactone -

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Basic information

Entry
Database: PDB / ID: 9y2h
TitleCrystal structure of MrtR bound to 7Z-3OH-C14 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
Biological speciesMesorhizobium tianshanense (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.06 Å
AuthorsStoutland, I.M. / Blackwell, H.E. / Buller, A.R. / Bingman, C.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)2R35GM131817 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
DepositionSep 1, 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

Downloads & links

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Assembly

Deposited unit
B: MrtR
A: MrtR
C: MrtR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,8056
Polymers81,8283
Non-polymers9763
Water25214
1
B: MrtR
C: MrtR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2034
Polymers54,5522
Non-polymers6512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-13 kcal/mol
Surface area20650 Å2
MethodPISA
2
A: MrtR
hetero molecules

A: MrtR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2034
Polymers54,5522
Non-polymers6512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area3640 Å2
ΔGint-15 kcal/mol
Surface area20960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.100, 120.793, 122.601
Angle α, β, γ (deg.)90.00, 98.58, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein MrtR


Mass: 27276.066 Da / Num. of mol.: 3
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
#2: Chemical ChemComp-A1CRU / (3R,7Z)-3-hydroxy-N-[(3S)-2-oxo-2,3-dihydrofuran-3-yl]tetradec-7-enamide / N-(3-hydroxy-7-cis tetradecenoyl)-L-Homoserine lactone


Mass: 325.443 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H31NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 3 Å3/Da / Density % sol: 59.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: magnesium chloride, calcium chloride, sodium HEPES, MOPS, ethylene glycol, PEG 8000, N-(3-hydroxy-7-cis-tetradecenoyl)-L-homoserine lactone

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.979338 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 17, 2025
RadiationMonochromator: Double Crystal Monochromator; Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979338 Å / Relative weight: 1
ReflectionResolution: 3.06→42.8 Å / Num. obs: 17089 / % possible obs: 93.2 % / Redundancy: 6.07 % / CC1/2: 0.954 / Net I/σ(I): 4
Reflection shellResolution: 3.06→3.111 Å / Num. unique obs: 909 / CC1/2: 0.35 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.06→42.8 Å / Cor.coef. Fo:Fc: 0.874 / Cor.coef. Fo:Fc free: 0.825 / SU B: 76.921 / SU ML: 0.569 / Cross valid method: THROUGHOUT / ESU R Free: 0.549 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29424 804 4.7 %RANDOM
Rwork0.25625 ---
obs0.25799 16275 93.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 62.303 Å2
Baniso -1Baniso -2Baniso -3
1--0.56 Å20 Å22.35 Å2
2---0.5 Å2-0 Å2
3---0.33 Å2
Refinement stepCycle: 1 / Resolution: 3.06→42.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5577 0 0 14 5591
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0125711
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165401
X-RAY DIFFRACTIONr_angle_refined_deg0.8421.8227777
X-RAY DIFFRACTIONr_angle_other_deg0.3261.77712388
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.735704
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.095541
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.03610887
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0350.2876
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.026777
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021314
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7572.8962825
X-RAY DIFFRACTIONr_mcbond_other0.7572.8962825
X-RAY DIFFRACTIONr_mcangle_it1.4085.2063526
X-RAY DIFFRACTIONr_mcangle_other1.4085.2063527
X-RAY DIFFRACTIONr_scbond_it0.4582.7662886
X-RAY DIFFRACTIONr_scbond_other0.4582.7662887
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.9335.1024252
X-RAY DIFFRACTIONr_long_range_B_refined2.90527.426409
X-RAY DIFFRACTIONr_long_range_B_other2.90527.416410
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.06→3.137 Å
RfactorNum. reflection% reflection
Rfree0.373 67 -
Rwork0.378 1270 -
obs--99.78 %
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)
11.7152-0.21050.00041.050.03951.10380.01140.0102-0.1685-0.0057-0.15560.13130.0889-0.06580.14420.64650.0452-0.16070.3144-0.00910.09446.0471-9.796630.9782
20.50470.22090.332.9686-0.03510.68170.04640.06450.0034-0.1503-0.14050.2269-0.0229-0.10740.09410.53030.0706-0.20220.4046-0.04910.102316.2569-33.007849.825
31.0451-0.1381-0.44380.34490.24152.2689-0.1056-0.0072-0.0684-0.2345-0.07350.047-0.44260.58340.17910.6685-0.1175-0.19070.49860.06010.069619.27397.233914.3128
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B5 - 301
2X-RAY DIFFRACTION2A8 - 301
3X-RAY DIFFRACTION3C6 - 301

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