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- PDB-9nj8: Crystal structure of apo Vibrio cholerae CqsR with D198N mutation -

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Basic information

Entry
Database: PDB / ID: 9nj8
TitleCrystal structure of apo Vibrio cholerae CqsR with D198N mutation
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
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 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
B: histidine kinase


Theoretical massNumber of molelcules
Total (without water)48,4122
Polymers48,4122
Non-polymers00
Water1448
1
A: histidine kinase


Theoretical massNumber of molelcules
Total (without water)24,2061
Polymers24,2061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: histidine kinase


Theoretical massNumber of molelcules
Total (without water)24,2061
Polymers24,2061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.706, 111.706, 75.735
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein histidine kinase


Mass: 24205.787 Da / Num. of mol.: 2 / Mutation: D198N
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
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: 2.79 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 2.0 M sodium formate, 2% glycerol

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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: Sep 4, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.540562 Å / Relative weight: 1
ReflectionResolution: 2.5→19.88 Å / Num. obs: 19154 / % possible obs: 99.7 % / Redundancy: 12.7 % / CC1/2: 0.999 / Rpim(I) all: 0.037 / Net I/σ(I): 6.38
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rpim(I) all% possible all
2.5-2.5913.41.3719210.760.22499.9
2.59-2.713.41.8819220.8220.2100
2.7-2.8213.32.519220.8680.184100
2.82-2.9713.23.6919220.9510.144100
2.97-3.1613.15.7719220.9660.109100
3.16-3.411312.0919220.9840.067100
3.41-3.7712.824.4319220.9910.042100
3.77-4.3312.643.5119200.9970.02499.9
4.33-5.512.166.4319200.9990.01599.9
5.5-19.8810.382.66186110.00996.8

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
PHASERphasing
CrysalisProdata reduction
CrysalisProdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→19.88 Å / Cross valid method: FREE R-VALUE / σ(F): 0.03 / Phase error: 28.21 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2628 1678 10.31 %
Rwork0.2171 --
obs0.2268 16277 85.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3122 0 0 8 3130
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043188
X-RAY DIFFRACTIONf_angle_d0.5564330
X-RAY DIFFRACTIONf_dihedral_angle_d15.3191116
X-RAY DIFFRACTIONf_chiral_restr0.041476
X-RAY DIFFRACTIONf_plane_restr0.004558
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.570.38781140.361959X-RAY DIFFRACTION62
2.57-2.660.36271160.33741107X-RAY DIFFRACTION69
2.66-2.750.37061060.312995X-RAY DIFFRACTION64
2.75-2.860.32951240.30631087X-RAY DIFFRACTION69
2.86-2.990.36861260.29441094X-RAY DIFFRACTION69
2.99-3.150.35041230.26611132X-RAY DIFFRACTION72
3.15-3.340.34871320.25341221X-RAY DIFFRACTION78
3.34-3.60.31721420.24531352X-RAY DIFFRACTION84
3.6-3.960.24651440.21861379X-RAY DIFFRACTION87
3.96-4.530.21031610.17481397X-RAY DIFFRACTION87
4.53-5.680.22251610.18281432X-RAY DIFFRACTION89
5.69-19.880.24131720.18861501X-RAY DIFFRACTION89
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)
13.02711.2603-0.00981.96231.12440.8799-0.42780.04810.78580.04230.14610.5555-0.2163-0.46130.22960.4309-0.0223-0.13370.38590.16520.6953-55.6768-6.77842.4696
22.8003-2.08622.35375.01611.26886.8111-0.1451-0.41650.98020.8643-0.1248-0.9946-0.3229-0.11630.21410.4906-0.0057-0.18580.44620.16170.6953-37.79841.85428.8526
30.76150.95030.284.57341.26761.6858-0.1161-0.8351-0.17370.0947-0.0812-0.13220.42050.1925-0.60680.39790.1248-0.02040.7730.42420.7976-27.8234-4.5645.8126
41.78970.2608-0.42921.38410.54130.3765-0.5491-0.62820.52380.2911-0.03230.201-0.07460.9388-0.06310.5041-0.0299-0.29731.02370.38940.9697-32.6556-6.753213.6172
54.43371.4977-2.80461.6789-1.4084.7232-0.1581-0.2457-0.28250.1004-0.3155-0.47740.20830.36520.59740.42470.0123-0.07740.31520.11060.6527-41.1469-10.80182.8098
62.1504-0.85261.40262.06930.8242.015-0.35970.1228-0.5302-0.340.4952-0.0929-0.0732-0.2450.05450.6543-0.21770.1470.47960.01610.7915-60.7234-21.24832.8242
71.9698-1.33521.03561.3620.09391.9071-0.4226-0.1344-0.07870.0110.15960.1604-0.0231-0.39240.19120.43880.04280.04770.3894-0.04930.4153-64.6432-0.98484.7657
81.31341.7086-0.18732.5695-0.10871.8693-0.1239-0.85080.44620.3474-0.36340.56350.0519-1.10030.28340.50720.04910.18280.8494-0.22720.6558-81.13773.12777.969
91.1527-0.3730.91533.0040.84033.3118-0.4053-0.3928-0.05350.3109-0.1420.4775-0.5911-0.66080.49420.51010.10670.07130.5067-0.14060.4595-70.28797.44865.0095
105.73920.41211.51533.8366-0.0486.1644-0.0481-0.16220.3675-0.53680.51510.5818-0.209-0.334-0.41040.7192-0.0797-0.050.3577-0.00550.7696-53.61518.38145.391
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 46 through 75 )
2X-RAY DIFFRACTION2chain 'A' and (resid 76 through 106 )
3X-RAY DIFFRACTION3chain 'A' and (resid 107 through 125 )
4X-RAY DIFFRACTION4chain 'A' and (resid 126 through 145 )
5X-RAY DIFFRACTION5chain 'A' and (resid 146 through 214 )
6X-RAY DIFFRACTION6chain 'A' and (resid 215 through 259 )
7X-RAY DIFFRACTION7chain 'B' and (resid 44 through 93 )
8X-RAY DIFFRACTION8chain 'B' and (resid 94 through 154 )
9X-RAY DIFFRACTION9chain 'B' and (resid 155 through 215 )
10X-RAY DIFFRACTION10chain 'B' and (resid 216 through 259 )

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