PDB-9nia: Crystal structure of Vibrio cholerae CqsR bound to ethanolamine

ID or keywords:

Entry

Database: PDB / ID: 9nia

Title

Crystal structure of Vibrio cholerae CqsR bound to ethanolamine

Components

histidine kinase

Keywords

SIGNALING PROTEIN / Quorum-sensing receptor / Double Cache domain / Periplasmic ligand-binding receptor / 2-amino alcohol receptor

Function / homology

Function and homology information

histidine kinase / phosphorelay sensor kinase activity / hydrolase activity / membrane
Similarity search - Function

Biological species

Vibrio cholerae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.55 Å

Authors

Guarnaccia, A.M. / Capodagli, G.C. / Neiditch, M.B.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	AI121337	United States
National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS)	TL1TR003019	United States

Citation

Journal: To Be Published
Title: Structure-function studies of Vibrio cholerae quorum-sensing receptor CqsR signal recognition
Authors: Guarnaccia, A.M. / Steenhaut, A.D. / Olenic, S.D. / Na, J. / Perez, L.J. / Ng, W.L. / Neiditch, M.B.

History

Deposition	Feb 25, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 2, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9nia.cif.gz	142.9 KB	Display	PDBx/mmCIF format
PDB format	pdb9nia.ent.gz	112.7 KB	Display	PDB format
PDBx/mmJSON format	9nia.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9nia_validation.pdf.gz	649.6 KB	Display	wwPDB validaton report
Full document	9nia_full_validation.pdf.gz	651.3 KB	Display
Data in XML	9nia_validation.xml.gz	13.1 KB	Display
Data in CIF	9nia_validation.cif.gz	17.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ni/9nia ftp://data.pdbj.org/pub/pdb/validation_reports/ni/9nia	HTTPS FTP

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Related structure data

Related structure data	9nitC 9nivC 9nj8C 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
Related items in Molecule of the Month	#190 - Oct 2015 Two-component Systems similarity (13) #183 - Mar 2015 Phototropin similarity (8) #97 - Jan 2008 Circadian Clock Proteins similarity (1)

Deposited unit

A: histidine kinase

hetero molecules

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

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	121.811, 121.811, 70.711
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	98
Space group name H-M	I4₁22

Components on special symmetry positions

ID	Model	Components
1	1	A-426- HOH
2	1	A-528- HOH

#1: Protein	histidine kinase Mass: 24206.773 Da / Num. of mol.: 1 / Fragment: residues 44-260 (46-262 Uniprot numbering) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: C6706 / Gene: VC_1831 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9KR16, histidine kinase
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-ETA / ETHANOLAMINE Type: L-peptide COOH carboxy terminus / Mass: 61.083 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₇NO / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.69 Å³/Da / Density % sol: 54.2 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 1.8 M lithium chloride, 0.1 M bicine pH 9.0, 10% PEG 6000

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SSRL

/ Beamline: BL9-2 / Wavelength: 0.97946 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 15, 2024

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97946 Å / Relative weight: 1

Reflection

Resolution: 1.55→50 Å / Num. obs: 38762 / % possible obs: 100 % / Redundancy: 12.6 % / CC_1/2: 0.997 / CC star: 0.999 / R_merge(I) obs: 0.085 / R_pim(I) all: 0.025 / R_rim(I) all: 0.089 / Χ²: 1.066 / Net I/σ(I): 5.8

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	CC star	R_pim(I) all	R_rim(I) all	Χ²	% possible all
1.55-1.58	8.3	1.403	1899	0.56	0.847	0.515	1.498	0.432	100
1.58-1.61	11.2	1.27	1926	0.711	0.912	0.395	1.331	0.453	100
1.61-1.64	12.6	1.091	1889	0.762	0.93	0.318	1.137	0.469	100
1.64-1.67	13	0.942	1917	0.83	0.952	0.269	0.98	0.472	100
1.67-1.71	13.1	0.82	1908	0.873	0.965	0.234	0.853	0.505	100
1.71-1.75	13	0.683	1920	0.909	0.976	0.195	0.71	0.543	100
1.75-1.79	12.7	0.527	1913	0.941	0.985	0.153	0.549	0.59	100
1.79-1.84	11.9	0.43	1905	0.956	0.989	0.129	0.45	0.665	99.9
1.84-1.89	13.6	0.365	1930	0.971	0.993	0.102	0.379	0.754	100
1.89-1.95	13.5	0.279	1928	0.98	0.995	0.078	0.29	0.879	100
1.95-2.02	13.2	0.224	1933	0.989	0.997	0.063	0.233	1.02	100
2.02-2.1	12.9	0.192	1928	0.991	0.998	0.055	0.2	1.142	99.9
2.1-2.2	11.9	0.162	1925	0.991	0.998	0.048	0.169	1.364	99.8
2.2-2.32	13.5	0.149	1929	0.993	0.998	0.042	0.155	1.516	100
2.32-2.46	13.4	0.128	1938	0.994	0.999	0.036	0.133	1.566	100
2.46-2.65	13.3	0.109	1959	0.996	0.999	0.031	0.114	1.713	100
2.65-2.92	12.3	0.095	1951	0.996	0.999	0.028	0.099	1.854	100
2.92-3.34	13.7	0.078	1977	0.997	0.999	0.022	0.081	1.916	100
3.34-4.21	12.5	0.06	1991	0.998	1	0.018	0.063	1.824	100
4.21-50	12.7	0.042	2096	0.999	1	0.012	0.044	1.127	99.8

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Processing

Software

Name	Version	Classification
PHENIX	1.21.2_5419	refinement
HKL-3000		data scaling
PHASER		phasing
HKL-3000		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.55→38.52 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.11 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2075	1999	5.16 %
R_work	0.1831	-	-
obs	0.1843	38730	99.91 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.55→38.52 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1694	0	5	137	1836

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	1770
X-RAY DIFFRACTION	f_angle_d	0.933	2419
X-RAY DIFFRACTION	f_dihedral_angle_d	15.608	638
X-RAY DIFFRACTION	f_chiral_restr	0.062	265
X-RAY DIFFRACTION	f_plane_restr	0.01	318

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 (%)
1.55-1.59	0.3287	139	0.2971	2550	X-RAY DIFFRACTION	100
1.59-1.63	0.271	142	0.2431	2600	X-RAY DIFFRACTION	100
1.63-1.68	0.2149	140	0.2197	2580	X-RAY DIFFRACTION	100
1.68-1.73	0.2107	141	0.2111	2593	X-RAY DIFFRACTION	100
1.73-1.79	0.213	142	0.2054	2606	X-RAY DIFFRACTION	100
1.79-1.87	0.2347	142	0.207	2598	X-RAY DIFFRACTION	100
1.87-1.95	0.2285	141	0.1929	2598	X-RAY DIFFRACTION	100
1.95-2.05	0.2008	141	0.1825	2604	X-RAY DIFFRACTION	100
2.05-2.18	0.1952	142	0.1782	2607	X-RAY DIFFRACTION	100
2.18-2.35	0.228	144	0.1816	2633	X-RAY DIFFRACTION	100
2.35-2.59	0.1951	143	0.1909	2638	X-RAY DIFFRACTION	100
2.59-2.96	0.2765	144	0.1898	2649	X-RAY DIFFRACTION	100
2.96-3.73	0.1916	145	0.1853	2683	X-RAY DIFFRACTION	100
3.73-38.52	0.1791	153	0.1593	2792	X-RAY DIFFRACTION	100

Refinement TLS params.

Method: refined / Origin x: 18.1534 Å / Origin y: 0.5449 Å / Origin z: -16.5362 Å

	11	12	13	21	22	23	31	32	33
T	0.1152 Å²	0.0029 Å²	-0.0245 Å²	-	0.1934 Å²	0.0339 Å²	-	-	0.2904 Å²
L	1.5343 °²	0.0464 °²	-0.6628 °²	-	0.4965 °²	-0.539 °²	-	-	3.1002 °²
S	0.05 Å °	0.2032 Å °	0.1593 Å °	-0.0206 Å °	-0.0859 Å °	-0.0046 Å °	-0.0333 Å °	0.2944 Å °	0.0261 Å °

Refinement TLS group

Selection details: all

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