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- PDB-10zi: Crystal structure of MrtR bound to 3O-C8 homoserine lactone and t... -

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Basic information

Entry
Database: PDB / ID: 10zi
TitleCrystal structure of MrtR bound to 3O-C8 homoserine lactone and tetraethylene glycol
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: 1.22 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
DepositionFeb 12, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1447
Polymers27,2761
Non-polymers8686
Water6,702372
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)126.434, 35.728, 61.941
Angle α, β, γ (deg.)90.00, 112.13, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-685-

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 , 6 types, 378 molecules

#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-LAE / 3-OXO-OCTANOIC ACID (2-OXO-TETRAHYDRO-FURAN-3-YL)-AMIDE / N-(3-OXO-OCTANAL-1-YL)-HOMOSERINE LACTONE


Mass: 241.284 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H19NO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 372 / 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: 2.38 Å3/Da / Density % sol: 48.22 %
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-oxoctanoyl-L-homoserine lactone, DMSO

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.96546 Å
DetectorType: DECTRIS PILATUS4 X 4M / Detector: PIXEL / Date: Jul 24, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 1.22→58.56 Å / Num. obs: 70635 / % possible obs: 92.6 % / Redundancy: 6.4 % / CC1/2: 0.999 / Net I/σ(I): 11.5
Reflection shellResolution: 1.22→1.243 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 0.5 / Num. unique obs: 3460 / CC1/2: 0.681 / % possible all: 90.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.22→58.56 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.966 / SU B: 2.65 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19345 3487 5 %RANDOM
Rwork0.15539 ---
obs0.15726 66060 91.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.288 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20.21 Å2
2---0.18 Å20 Å2
3---0.04 Å2
Refinement stepCycle: 1 / Resolution: 1.22→58.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1945 0 34 372 2351
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0122443
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162348
X-RAY DIFFRACTIONr_angle_refined_deg1.631.8283352
X-RAY DIFFRACTIONr_angle_other_deg0.5931.8135413
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1515315
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.292524
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.37810407
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0830.2357
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023036
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02602
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_it4.7491.7641162
X-RAY DIFFRACTIONr_mcbond_other4.7231.7641162
X-RAY DIFFRACTIONr_mcangle_it6.7333.1851494
X-RAY DIFFRACTIONr_mcangle_other6.7343.1861495
X-RAY DIFFRACTIONr_scbond_it6.1122.0811281
X-RAY DIFFRACTIONr_scbond_other6.112.0831282
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.7873.6941852
X-RAY DIFFRACTIONr_long_range_B_refined15.19322.662759
X-RAY DIFFRACTIONr_long_range_B_other12.52619.62626
X-RAY DIFFRACTIONr_rigid_bond_restr3.53234791
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.222→1.254 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.435 222 -
Rwork0.423 3967 -
obs--74.63 %

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