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

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Basic information

Entry
Database: PDB / ID: 9koo
TitleLigand binding domain of Pseudomonas Aeruginosa PAO1 chemoreceptor PctA in complex with MHF
ComponentsMethyl-accepting chemotaxis protein PctA
KeywordsSIGNALING PROTEIN / PCTA / MHF / Complex / Methyl-accepting chemotaxis protein
Function / homology
Function and homology information


amino acid binding / response to amino acid / chemotaxis / transmembrane signaling receptor activity / signal transduction / plasma membrane
Similarity search - Function
Double Cache domain 1 / Cache domain / Periplasmic sensor-like domain superfamily / Chemotaxis methyl-accepting receptor / 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). / Target SNARE coiled-coil homology domain / HAMP domain ...Double Cache domain 1 / Cache domain / Periplasmic sensor-like domain superfamily / Chemotaxis methyl-accepting receptor / 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). / Target SNARE coiled-coil homology domain / 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 / Methyl-accepting chemotaxis protein PctA
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 PctA in complex with MHF
Authors: Songying, O. / Yanbo, Z. / Lei, Z. / Xinyu, Q.
History
DepositionNov 21, 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: Methyl-accepting chemotaxis protein PctA
B: Methyl-accepting chemotaxis protein PctA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7774
Polymers60,5482
Non-polymers2282
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-9 kcal/mol
Surface area20490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.972, 76.166, 117.802
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Methyl-accepting chemotaxis protein PctA


Mass: 30274.219 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: pctA, PA4309 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G3XD24
#2: Chemical ChemComp-4XX / 4-hydroxy-5-methylfuran-3(2H)-one


Mass: 114.099 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H6O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 2.63 Å3/Da / Density % sol: 53.22 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / Details: 2.0 M ammonium sulfate

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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: 2.7→36.24 Å / Num. obs: 18133 / % possible obs: 99.26 % / Redundancy: 7 % / CC1/2: 0.999 / CC star: 1 / Net I/σ(I): 11.16
Reflection shellResolution: 2.7→2.7 Å / Num. unique obs: 25707 / CC1/2: 0.999

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5T65

5t65


Resolution: 2.7→36.24 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2595 1404 7.8 %
Rwork0.2066 --
obs-18008 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→36.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3594 0 16 178 3788
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013700
X-RAY DIFFRACTIONf_angle_d1.2215044
X-RAY DIFFRACTIONf_dihedral_angle_d14.7791344
X-RAY DIFFRACTIONf_chiral_restr0.225581
X-RAY DIFFRACTIONf_plane_restr0.007649
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.80.29241460.2231604X-RAY DIFFRACTION98
2.8-2.910.28861250.23211614X-RAY DIFFRACTION98
2.91-3.040.33371350.2391629X-RAY DIFFRACTION99
3.04-3.20.30341430.2221644X-RAY DIFFRACTION100
3.2-3.40.2581450.21131627X-RAY DIFFRACTION100
3.4-3.660.2911330.20871664X-RAY DIFFRACTION100
3.66-4.030.24561410.19071680X-RAY DIFFRACTION100
4.03-4.610.23741400.16641666X-RAY DIFFRACTION100
4.61-5.810.23371510.18041696X-RAY DIFFRACTION100
5.81-36.240.22751450.20161780X-RAY DIFFRACTION99

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