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- PDB-9heh: Structure of the ligand binding domain of the chemoreceptor MkcA ... -

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Basic information

Entry
Database: PDB / ID: 9heh
TitleStructure of the ligand binding domain of the chemoreceptor MkcA (DSOMK10_RS0100305) of Dickeya solani MK10 in complex with choline
ComponentsMethyl-accepting chemotaxis protein
KeywordsSIGNALING PROTEIN / chemotactic transducer / CHEMORECEPTOR / Ligand binding domain
Function / homologyCHOLINE ION / :
Function and homology information
Biological speciesDickeya solani MK10 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsGavira, J.A. / Rico-Jimenez, M. / Matilla, M.A.
Funding support Spain, 2items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)PID2019-103972GA-I00 Spain
Ministerio de Ciencia e Innovacion (MCIN)PID2020-116261GB-I00 Spain
CitationJournal: Microbiol Res / Year: 2025
Title: Acetylcholine chemotaxis in global bacterial plant pathogens.
Authors: Gavira, J.A. / Gilabert, M.J. / Santamaria-Hernando, S. / Molina-Ollero, A. / Rico-Jimenez, M. / Cabrera, J.J. / Lopez-Solanilla, E. / Matilla, M.A.
History
DepositionNov 14, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2025Group: Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methyl-accepting chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3857
Polymers33,8761
Non-polymers5096
Water4,810267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-1 kcal/mol
Surface area13870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.714, 67.185, 53.824
Angle α, β, γ (deg.)90.00, 97.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Methyl-accepting chemotaxis protein


Mass: 33876.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dickeya solani MK10 (bacteria)
Gene: trg_19, FGLHLNJM_03480, HAT90_03954, I2625_07850, O0557_07220
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0AAP1TQ45

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Non-polymers , 5 types, 273 molecules

#2: Chemical ChemComp-CHT / CHOLINE ION


Mass: 104.171 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H14NO / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 2.22 Å3/Da / Density % sol: 44.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M Tris hydrochloride pH 8.5, 30% w/v PEG 4K

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Nitrogen blowing / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 8, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.5→67.18 Å / Num. obs: 47135 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.041 / Rrim(I) all: 0.107 / Χ2: 1.01 / Net I/σ(I): 11.2 / Num. measured all: 317463
Reflection shellResolution: 1.5→1.53 Å / % possible obs: 99.9 % / Redundancy: 6.8 % / Rmerge(I) obs: 1.658 / Num. measured all: 15953 / Num. unique obs: 2329 / CC1/2: 0.592 / Rpim(I) all: 0.682 / Rrim(I) all: 1.795 / Χ2: 1.02 / Net I/σ(I) obs: 1.2

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→53.35 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2016 2368 5.03 %
Rwork0.1739 --
obs0.1753 47077 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→53.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2206 0 32 267 2505
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072450
X-RAY DIFFRACTIONf_angle_d0.9073356
X-RAY DIFFRACTIONf_dihedral_angle_d17.343969
X-RAY DIFFRACTIONf_chiral_restr0.058369
X-RAY DIFFRACTIONf_plane_restr0.007441
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.530.32571640.32342585X-RAY DIFFRACTION100
1.53-1.560.32921520.30232609X-RAY DIFFRACTION100
1.56-1.60.3031370.27962641X-RAY DIFFRACTION100
1.6-1.640.30691470.25082587X-RAY DIFFRACTION100
1.64-1.680.22321380.23952649X-RAY DIFFRACTION100
1.68-1.730.23051470.2312597X-RAY DIFFRACTION100
1.73-1.790.24631320.21142628X-RAY DIFFRACTION100
1.79-1.850.26331480.20192614X-RAY DIFFRACTION100
1.85-1.930.23371220.19882642X-RAY DIFFRACTION100
1.93-2.020.19831310.16952628X-RAY DIFFRACTION100
2.02-2.120.20021300.15832637X-RAY DIFFRACTION100
2.12-2.260.18781440.17082621X-RAY DIFFRACTION100
2.26-2.430.20581300.16432634X-RAY DIFFRACTION100
2.43-2.670.19841370.16232639X-RAY DIFFRACTION100
2.67-3.060.2311180.17082668X-RAY DIFFRACTION100
3.06-3.860.18041640.15192622X-RAY DIFFRACTION100
3.86-53.350.13871270.13772708X-RAY DIFFRACTION99
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)
10.2634-0.03220.28011.01360.00630.6877-0.129-0.02740.03250.53030.26520.3927-0.4737-0.1870.03810.28220.04930.03010.17620.00510.1742-19.707814.549320.5105
20.50060.09030.2671.0243-0.02330.7902-0.01680.0117-0.0680.12230.0418-0.0581-0.0394-0.0430.00210.12360.00410.00030.12440.00040.1331-13.9334-9.968120.6663
3-0.0284-0.07910.3380.2556-0.54970.49730.01210.0879-0.05720.03960.0070.0279-0.04390.0884-00.20310.0109-0.030.17390.00630.1612-15.210519.15076.0858
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 23 through 70 )
2X-RAY DIFFRACTION2chain 'A' and (resid 71 through 210 )
3X-RAY DIFFRACTION3chain 'A' and (resid 211 through 306 )

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