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- PDB-7prr: Structure of the ligand binding domain of the PctD (PA4633) chemo... -

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Basic information

Entry
Database: PDB / ID: 7prr
TitleStructure of the ligand binding domain of the PctD (PA4633) chemoreceptor of Pseudomonas aeruginosa PAO1 in complex with acetylcholine
ComponentsProbable chemotaxis transducer
KeywordsSIGNALING PROTEIN / Ligand binding domain / Pseudomonas aeruginosa / chemotactic transducer
Function / homology
Function and homology information


chemotaxis / membrane => GO:0016020 / signal transduction
Similarity search - Function
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
ACETYLCHOLINE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Probable chemotaxis transducer
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGavira, J.A. / Matilla, M.A. / Martin-Mora, D. / Krell, T.
Funding support Spain, 2items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBIO2016-74875-P Spain
Spanish Ministry of Economy and CompetitivenessBIO2016-76779-P Spain
CitationJournal: Mbio / Year: 2022
Title: Chemotaxis of the Human Pathogen Pseudomonas aeruginosa to the Neurotransmitter Acetylcholine.
Authors: Matilla, M.A. / Velando, F. / Tajuelo, A. / Martin-Mora, D. / Xu, W. / Sourjik, V. / Gavira, J.A. / Krell, T.
History
DepositionSep 22, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 11, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable chemotaxis transducer
B: Probable chemotaxis transducer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,94610
Polymers76,9062
Non-polymers1,0398
Water8,143452
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6460 Å2
ΔGint26 kcal/mol
Surface area25870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.288, 102.650, 104.848
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Probable chemotaxis transducer


Mass: 38453.246 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Ligand binding domain
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: PA4633 / Plasmid: PET28B+
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9HVF8

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Non-polymers , 5 types, 460 molecules

#2: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-ACH / ACETYLCHOLINE


Mass: 146.207 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H16NO2 / Feature type: SUBJECT OF INVESTIGATION / Comment: neurotransmitter*YM
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 452 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.13 Å3/Da / Density % sol: 42.24 %
Crystal growTemperature: 293 K / Method: counter-diffusion / pH: 4.6
Details: 0.2 M Ammonium acetate, 0.1 M Sodium acetate trihydrate pH 4.6, 30% w/v Polyethylene glycol 4,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.8→47.48 Å / Num. obs: 62249 / % possible obs: 99 % / Redundancy: 4.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.043 / Rrim(I) all: 0.096 / Net I/σ(I): 10.7 / Num. measured all: 280823 / Scaling rejects: 11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.8-1.844.51.0171671036950.5810.5151.1471.299.7
9-47.484.30.02224145560.9980.0110.02442.895.5

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.19-4092refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7PRQ

7prq


Resolution: 1.8→47.48 Å / SU ML: 0.2018 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.8005
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.207 3166 5.09 %
Rwork0.1668 58994 -
obs0.1689 62160 98.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.09 Å2
Refinement stepCycle: LAST / Resolution: 1.8→47.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4776 0 68 452 5296
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01215184
X-RAY DIFFRACTIONf_angle_d1.09067062
X-RAY DIFFRACTIONf_chiral_restr0.0624762
X-RAY DIFFRACTIONf_plane_restr0.0088950
X-RAY DIFFRACTIONf_dihedral_angle_d16.1222013
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.830.32031270.28892558X-RAY DIFFRACTION99.48
1.83-1.860.29331210.28062575X-RAY DIFFRACTION99.59
1.86-1.890.32311350.25732549X-RAY DIFFRACTION99.11
1.89-1.920.31081330.25032543X-RAY DIFFRACTION99.33
1.92-1.950.29641280.24452554X-RAY DIFFRACTION99.19
1.95-1.990.2481510.22332559X-RAY DIFFRACTION99.67
1.99-2.030.24451440.21652543X-RAY DIFFRACTION99.15
2.03-2.080.29691230.20372548X-RAY DIFFRACTION98.78
2.08-2.120.24151260.19022578X-RAY DIFFRACTION99.45
2.12-2.180.21561560.17322541X-RAY DIFFRACTION99.48
2.18-2.240.21851460.16952567X-RAY DIFFRACTION99.34
2.24-2.30.23341460.16352561X-RAY DIFFRACTION99.49
2.3-2.380.20841290.16062572X-RAY DIFFRACTION99.16
2.38-2.460.20811270.15512567X-RAY DIFFRACTION99.59
2.46-2.560.24061400.15612576X-RAY DIFFRACTION99.09
2.56-2.680.19941330.16162568X-RAY DIFFRACTION98.68
2.68-2.820.21221500.15212556X-RAY DIFFRACTION98.76
2.82-2.990.17481600.15512556X-RAY DIFFRACTION98.26
2.99-3.220.22211570.16512537X-RAY DIFFRACTION98.11
3.22-3.550.17861220.15042571X-RAY DIFFRACTION97.36
3.55-4.060.15491180.13832588X-RAY DIFFRACTION96.89
4.06-5.120.15481420.12672575X-RAY DIFFRACTION96.25
5.12-47.480.21661520.17992652X-RAY DIFFRACTION94.73

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