PDB-11bm: Crystal structure of MrtR bound to 3O-C8 homoserine lactone

ID or keywords:

Entry

Database: PDB / ID: 11bm

Title

Crystal structure of MrtR bound to 3O-C8 homoserine lactone

Components

MrtR

Keywords

TRANSCRIPTION / quorum sensing receptor

Function / homology

Function and homology information

regulation of DNA-templated transcription / DNA binding
Similarity search - Function

Biological species

Mesorhizobium tianshanense (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.442 Å

Authors

Stoutland, I.M. / Bingman, C.A. / Elias, M.H. / Blackwell, H.E.

Funding support

United States, 1items

Citation

Journal: 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

Deposition	Feb 16, 2026	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 23, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	11bm.cif.gz	151.5 KB	Display	PDBx/mmCIF format
PDB format	pdb11bm.ent.gz	90.8 KB	Display	PDB format
PDBx/mmJSON format	11bm.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/1b/11bm ftp://data.pdbj.org/pub/pdb/validation_reports/1b/11bm	HTTPS FTP

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Related structure data

Related structure data	10ziC 9y2hC 9zpjC 9zz0C C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: MrtR

hetero molecules

27.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: cross-linking

Unit cell

Length a, b, c (Å)	126.334, 35.554, 61.964
Angle α, β, γ (deg.)	90.000, 112.512, 90.000
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-575- HOH

#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
#2: 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
#3: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.36 Å³/Da / Density % sol: 47.81 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop 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

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.96546 Å
Detector	Type: DECTRIS PILATUS4 X 4M / Detector: PIXEL / Date: Jul 24, 2025
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.96546 Å / Relative weight: 1
Reflection	Resolution: 1.442→57.2 Å / Num. obs: 46325 / % possible obs: 100 % / Redundancy: 6.7 % / CC_1/2: 0.998 / Net I/σ(I): 10.8
Reflection shell	Resolution: 1.442→1.466 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 0.6 / Num. unique obs: 2324 / CC_1/2: 0.402 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0430	refinement
PDB_EXTRACT		data extraction
autoPROC		data reduction
autoPROC		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.442→57.2 Å / Cor.coef. F_o:F_c: 0.967 / Cor.coef. F_o:F_c free: 0.949 / SU B: 5.117 / SU ML: 0.08 / Cross valid method: FREE R-VALUE / ESU R: 0.079 / ESU R Free: 0.075
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2319	2318	5.047 %
R_work	0.1819	43609	-
all	0.184	-	-
obs	-	45927	99.184 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 30.194 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.936 Å²	-0 Å²	0.227 Å²
2-	-	1.935 Å²	0 Å²
3-	-	-	-0.139 Å²

Refinement step

Cycle: LAST / Resolution: 1.442→57.2 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1856	0	31	196	2083

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.012	1975
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	1867
X-RAY DIFFRACTION	r_angle_refined_deg	1.47	1.819	2687
X-RAY DIFFRACTION	r_angle_other_deg	0.532	1.789	4299
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.1	5	245
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	6.793	5	16
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.627	10	321
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.459	10	93
X-RAY DIFFRACTION	r_chiral_restr	0.074	0.2	293
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	2371
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	467
X-RAY DIFFRACTION	r_nbd_refined	0.22	0.2	423
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.198	0.2	1659
X-RAY DIFFRACTION	r_nbtor_refined	0.185	0.2	958
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.078	0.2	990
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.173	0.2	128
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.131	0.2	3
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.265	0.2	18
X-RAY DIFFRACTION	r_nbd_other	0.247	0.2	50
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.218	0.2	13
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.046	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	7.242	3.042	950
X-RAY DIFFRACTION	r_mcbond_other	7.236	3.041	950
X-RAY DIFFRACTION	r_mcangle_it	10.171	5.466	1190
X-RAY DIFFRACTION	r_mcangle_other	10.175	5.467	1191
X-RAY DIFFRACTION	r_scbond_it	8.594	3.425	1025
X-RAY DIFFRACTION	r_scbond_other	8.59	3.426	1026
X-RAY DIFFRACTION	r_scangle_it	12.213	6.116	1492
X-RAY DIFFRACTION	r_scangle_other	12.209	6.118	1493
X-RAY DIFFRACTION	r_lrange_it	17.081	34.953	2311
X-RAY DIFFRACTION	r_lrange_other	16.542	33.93	2278
X-RAY DIFFRACTION	r_rigid_bond_restr	3.54	3	3842

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.442-1.479	0.366	147	0.372	2940	X-RAY DIFFRACTION	90.5013
1.479-1.52	0.378	149	0.336	3128	X-RAY DIFFRACTION	99.2429
1.52-1.564	0.331	169	0.294	3045	X-RAY DIFFRACTION	99.9067
1.564-1.612	0.287	173	0.245	2961	X-RAY DIFFRACTION	100
1.612-1.665	0.234	151	0.215	2867	X-RAY DIFFRACTION	100
1.665-1.723	0.257	132	0.189	2815	X-RAY DIFFRACTION	100
1.723-1.788	0.238	142	0.176	2712	X-RAY DIFFRACTION	100
1.788-1.861	0.249	150	0.162	2550	X-RAY DIFFRACTION	100
1.861-1.944	0.244	115	0.167	2494	X-RAY DIFFRACTION	99.8469
1.944-2.039	0.253	138	0.153	2362	X-RAY DIFFRACTION	100
2.039-2.149	0.225	118	0.149	2275	X-RAY DIFFRACTION	100
2.149-2.279	0.252	122	0.162	2138	X-RAY DIFFRACTION	99.7793
2.279-2.436	0.192	97	0.152	2043	X-RAY DIFFRACTION	99.7669
2.436-2.631	0.185	103	0.14	1877	X-RAY DIFFRACTION	100
2.631-2.881	0.19	89	0.157	1742	X-RAY DIFFRACTION	100
2.881-3.22	0.2	104	0.171	1572	X-RAY DIFFRACTION	100
3.22-3.717	0.196	81	0.171	1395	X-RAY DIFFRACTION	100
3.717-4.547	0.244	71	0.169	1191	X-RAY DIFFRACTION	99.9208
4.547-6.41	0.311	46	0.225	937	X-RAY DIFFRACTION	100
6.41-57.2	0.223	21	0.217	562	X-RAY DIFFRACTION	99.6581

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