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- PDB-9zz0: Crystal structure of MrtR bound to 3OH-C14 homoserine lactone -

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Basic information

Entry
Database: PDB / ID: 9zz0
TitleCrystal structure of MrtR bound to 3OH-C14 homoserine lactone
ComponentsMrtR
KeywordsTRANSCRIPTION / LuxR 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: 3.36 Å
AuthorsStoutland, I.M. / Blackwell, H.E. / Bingman, C.A.
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
DepositionJan 6, 2026Deposition 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
B: MrtR
C: MrtR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,8737
Polymers81,8283
Non-polymers1,0444
Water362
1
A: MrtR
B: MrtR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2695
Polymers54,5522
Non-polymers7173
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-15 kcal/mol
Surface area20480 Å2
MethodPISA
2
C: MrtR
hetero molecules

C: MrtR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2074
Polymers54,5522
Non-polymers6552
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3380 Å2
ΔGint-21 kcal/mol
Surface area20550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.039, 120.926, 122.537
Angle α, β, γ (deg.)90.00, 98.81, 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-A1C4G / (3R)-3-hydroxy-N-[(3S)-2-oxooxolan-3-yl]tetradecanamide


Mass: 327.459 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H33NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 58.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 50 mM imidazole, 50 mM MES, 30 mM MgCl2, 30 percent ethylene glycol, 5 percent PEG 8000, N-(3-hydroxy-tetradecanoyl)-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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979338 Å / Relative weight: 1
ReflectionResolution: 3.36→34.4 Å / Num. obs: 12733 / % possible obs: 92.2 % / Redundancy: 6.9 % / CC1/2: 0.93 / Net I/σ(I): 4.2
Reflection shellResolution: 3.36→3.419 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 519 / CC1/2: 0.324

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
PDB_EXTRACTdata extraction
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.36→34.4 Å / Cor.coef. Fo:Fc: 0.846 / Cor.coef. Fo:Fc free: 0.733 / SU B: 107.254 / SU ML: 0.734 / Cross valid method: THROUGHOUT / ESU R Free: 0.724 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30845 595 4.7 %RANDOM
Rwork0.25301 ---
obs0.25562 12137 92.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.684 Å2
Baniso -1Baniso -2Baniso -3
1--0.92 Å2-0 Å22.62 Å2
2--0.42 Å20 Å2
3----0.3 Å2
Refinement stepCycle: 1 / Resolution: 3.36→34.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5435 0 0 2 5437
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0125567
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165092
X-RAY DIFFRACTIONr_angle_refined_deg0.7211.7917620
X-RAY DIFFRACTIONr_angle_other_deg0.3011.75811650
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9945709
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.268529
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.84810768
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0320.2877
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.026660
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021254
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_it0.862.822845
X-RAY DIFFRACTIONr_mcbond_other0.862.822845
X-RAY DIFFRACTIONr_mcangle_it1.5965.0693551
X-RAY DIFFRACTIONr_mcangle_other1.5965.0683552
X-RAY DIFFRACTIONr_scbond_it0.4862.6422722
X-RAY DIFFRACTIONr_scbond_other0.4862.6422721
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.0144.8954070
X-RAY DIFFRACTIONr_long_range_B_refined3.24325.86243
X-RAY DIFFRACTIONr_long_range_B_other3.24325.86244
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.361→3.447 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 21 -
Rwork0.329 534 -
obs--55.61 %
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)
11.06040.4331-0.42150.602-0.08041.28-0.05920.0105-0.08690.11510.0120.0099-0.2924-0.43870.04720.53660.0991-0.150.5554-0.02480.08765.5336.95646.3713
21.28850.36180.05510.9367-0.07811.0612-0.0293-0.0477-0.1618-0.0276-0.1297-0.04740.0880.03610.15910.5734-0.0566-0.17960.3726-0.01010.119418.1077-10.800129.4615
30.6314-0.24960.16051.90930.06150.66840.0217-0.1369-0.00570.0294-0.0337-0.1672-0.05240.12650.01210.4763-0.0478-0.23760.45310.01390.13178.5432-33.960810.8511
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 301
2X-RAY DIFFRACTION2B3 - 302
3X-RAY DIFFRACTION3C4 - 301

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