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- PDB-9kp3: Ligand binding domain of Pseudomonas Aeruginosa PAO1 chemorecepto... -

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Basic information

Entry
Database: PDB / ID: 9kp3
TitleLigand binding domain of Pseudomonas Aeruginosa PAO1 chemoreceptor TlpQ in complex with MHF
ComponentsChemotaxis transducer
KeywordsSIGNALING PROTEIN / TlpQ / MHF / Complex / Methyl-accepting chemotaxis protein
Function / homology
Function and homology information


chemotaxis / signal transduction / plasma membrane
Similarity search - Function
Methyl-accepting chemotaxis protein-like, first PDC sensor domain / Methyl-accepting chemotaxis protein (MCP) signalling domain / Methyl-accepting chemotaxis protein (MCP) signalling domain / Bacterial chemotaxis sensory transducers domain profile. / Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer). / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain
Similarity search - Domain/homology
4-hydroxy-5-methylfuran-3(2H)-one / DI(HYDROXYETHYL)ETHER / Chemotaxis transducer
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.74 Å
AuthorsSongying, O. / Yanbo, Z. / Lei, Z. / Xinyu, Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Ligand binding domain of Pseudomonas Aeruginosa PAO1 chemoreceptor TlpQ in complex with MHF
Authors: Songying, O. / Yanbo, Z. / Lei, Z. / Xinyu, Q.
History
DepositionNov 22, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chemotaxis transducer
B: Chemotaxis transducer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,4544
Polymers79,2332
Non-polymers2202
Water2,522140
1
A: Chemotaxis transducer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7232
Polymers39,6171
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chemotaxis transducer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7312
Polymers39,6171
Non-polymers1141
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.800, 124.911, 58.335
Angle α, β, γ (deg.)90.00, 99.41, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Chemotaxis transducer / Methl-accepting chemotaxis protein TlpQ / HAMP domain-containing protein / Methyl-accepting chemotaxis protein


Mass: 39616.746 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: pctC_4, pctC_1, CAZ10_23540, CCBH4851_00485, GUL26_11790, IPC1295_00345, PAERUG_P19_London_7_VIM_2_05_10_05471
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2U2Y0U1
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-4XX / 4-hydroxy-5-methylfuran-3(2H)-one


Mass: 114.099 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.21 Å3/Da / Density % sol: 44.44 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / Details: 0.1M CHES pH 9.5, 20% (w/v) PEG8000

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Data collection

DiffractionMean temperature: 82 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.979183 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 2.74→40.31 Å / Num. obs: 18154 / % possible obs: 96.17 % / Redundancy: 4 % / CC1/2: 0.991 / CC star: 0.998 / Net I/σ(I): 6.52
Reflection shellResolution: 2.74→2.81 Å / Num. unique obs: 17465 / CC1/2: 0.991 / CC star: 0.998

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Processing

Software
NameVersionClassification
PHENIXv1.18.2-3874refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FU4

6fu4


Resolution: 2.74→40.31 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2587 1727 -
Rwork0.2221 --
obs-17465 96.17 %
Refinement stepCycle: LAST / Resolution: 2.74→40.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4413 0 15 140 4568
LS refinement shellResolution: 2.74→2.838 Å
RfactorNum. reflection% reflection
Rfree0.3776 157 -
Rwork0.3257 --
obs-1619 90.19 %

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