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- PDB-9niv: Crystal structure of Vibrio cholerae CqsR bound to serinol -

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Basic information

Entry
Database: PDB / ID: 9niv
TitleCrystal structure of Vibrio cholerae CqsR bound to serinol
Componentshistidine kinase
KeywordsSIGNALING 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
Methyl-accepting chemotaxis protein-like, first PDC sensor domain / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase-related protein, C-terminal / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Histidine kinase domain / Histidine kinase domain profile. / Response regulator receiver domain / cheY-homologous receiver domain ...Methyl-accepting chemotaxis protein-like, first PDC sensor domain / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase-related protein, C-terminal / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Histidine kinase domain / Histidine kinase domain profile. / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
2-AMINO-1,3-PROPANEDIOL / histidine kinase
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsGuarnaccia, A.M. / Neiditch, M.B.
Funding support United States, 2items
OrganizationGrant numberCountry
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
CitationJournal: 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
DepositionFeb 26, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3333
Polymers24,2071
Non-polymers1272
Water3,117173
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.139, 121.139, 70.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-420-

HOH

21A-526-

HOH

31A-572-

HOH

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Components

#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-SEL / 2-AMINO-1,3-PROPANEDIOL / SERINOL


Type: L-peptide linking / Mass: 91.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H9NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 2.66 Å3/Da / Density % sol: 53.8 %
Crystal growTemperature: 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

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU PhotonJet-S / Wavelength: 1.540562 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Apr 22, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.540562 Å / Relative weight: 1
ReflectionResolution: 1.75→21.64 Å / Num. obs: 26724 / % possible obs: 99.7 % / Redundancy: 8.8 % / CC1/2: 0.999 / Rpim(I) all: 0.03 / Net I/σ(I): 7.32
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rpim(I) all% possible all
1.75-1.813.61.5726260.5850.33997.9
1.81-1.895.42.3226790.7790.24599.9
1.89-1.988.24.1826810.9350.154100
1.98-2.0810.46.6526810.9680.104100
2.08-2.2210.59.9426810.9840.074100
2.22-2.3910.513.3726810.9910.055100
2.39-2.6410.518.9526810.9960.039100
2.64-3.0310.428.6126810.9980.026100
3.03-3.8510.152.8226810.9990.014100
3.85-21.648.774.09265210.00998.9

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
PHASERphasing
CrysalisProdata reduction
CrysalisProdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→21.64 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 22.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2212 1819 7.61 %
Rwork0.1847 --
obs0.1875 23907 89.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→21.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1695 0 7 173 1875
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071761
X-RAY DIFFRACTIONf_angle_d0.9242402
X-RAY DIFFRACTIONf_dihedral_angle_d15.153632
X-RAY DIFFRACTIONf_chiral_restr0.051263
X-RAY DIFFRACTIONf_plane_restr0.011314
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.80.31781110.29771365X-RAY DIFFRACTION73
1.8-1.850.32091280.25911468X-RAY DIFFRACTION78
1.85-1.910.29091220.25011491X-RAY DIFFRACTION79
1.91-1.980.27861230.2081549X-RAY DIFFRACTION82
1.98-2.060.24321420.19561647X-RAY DIFFRACTION88
2.06-2.150.22691380.17861768X-RAY DIFFRACTION93
2.15-2.260.23931510.18031771X-RAY DIFFRACTION94
2.26-2.410.22781460.17571743X-RAY DIFFRACTION93
2.41-2.590.24811430.18561759X-RAY DIFFRACTION92
2.59-2.850.20331450.18591781X-RAY DIFFRACTION93
2.85-3.260.21771510.19271830X-RAY DIFFRACTION95
3.26-4.110.1941560.16221911X-RAY DIFFRACTION98
4.11-21.640.18521630.16372005X-RAY DIFFRACTION98
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)
12.0841-0.0151-2.66920.2689-0.74557.73330.1045-0.14730.51130.05620.0410.0703-0.07270.415-0.14130.1237-0.0428-0.00830.2374-0.0230.206224.19853.419-6.4879
22.5292-0.37410.42940.9561-0.13870.53390.02840.58790.0458-0.0988-0.1151-0.20290.01230.34130.03980.07330.0609-0.04260.47650.13760.246928.206-2.0581-27.8011
33.99540.7083.37951.5498-0.30094.1502-0.02341.03270.0296-1.0305-0.14950.5235-0.15880.3719-0.09410.44580.1477-0.12550.90050.15270.278815.66171.5857-41.5449
45.8548-0.34710.83123.20861.29383.81960.05190.4759-0.4805-0.1973-0.16260.08330.40560.3149-0.01770.12790.04430.01560.27120.05140.146916.9599-5.9273-30.4884
50.87911.4202-0.68542.9465-0.40832.6955-0.06450.21310.43870.1722-0.1371-0.2034-0.5450.07310.17020.16630.011-0.0790.17470.08540.280115.17388.8257-22.6371
61.1561-0.1602-0.76160.1645-0.46564.28170.05430.09210.16740.069-0.07640.0085-0.08910.15320.00530.0707-0.0003-0.0380.10050.02150.146614.9293-1.1826-10.1135
73.8992-0.1561-0.58346.8057-3.42065.3837-0.04410.32490.2854-0.39780.11050.0709-0.08610.0945-0.05920.1619-0.0418-0.02270.1688-0.02640.14113.13415.34050.4188
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 44 through 75 )
2X-RAY DIFFRACTION2chain 'A' and (resid 76 through 106 )
3X-RAY DIFFRACTION3chain 'A' and (resid 107 through 121 )
4X-RAY DIFFRACTION4chain 'A' and (resid 122 through 149 )
5X-RAY DIFFRACTION5chain 'A' and (resid 150 through 168 )
6X-RAY DIFFRACTION6chain 'A' and (resid 169 through 242 )
7X-RAY DIFFRACTION7chain 'A' and (resid 243 through 260 )

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