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

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Basic information

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


chemotaxis / signal transduction / metal ion binding / plasma membrane
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 / PAS domain / Beta-Lactamase ...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 / PAS domain / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CHOLINE ION / Probable chemotaxis transducer
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 1.1May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)77,68412
Polymers76,9062
Non-polymers77710
Water5,621312
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6120 Å2
ΔGint18 kcal/mol
Surface area25330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.138, 104.864, 118.602
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

#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
#2: Chemical ChemComp-CHT / CHOLINE ION


Mass: 104.171 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H14NO / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 2.22 Å3/Da / Density % sol: 44.54 %
Crystal growTemperature: 293 K / Method: counter-diffusion
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: ALBA / Beamline: XALOC / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→118.6 Å / Num. obs: 48037 / % possible obs: 99.8 % / Redundancy: 4.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.055 / Rrim(I) all: 0.117 / Net I/σ(I): 10 / Num. measured all: 214721 / Scaling rejects: 105
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2-2.054.41.0434730.6170.5631.18799.7
8.94-118.63.80.0296290.9990.0160.03399.4

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Processing

Software
NameVersionClassification
PHENIX1.19-4092refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: RaptorX

Resolution: 2→78.56 Å / SU ML: 0.2114 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.956
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2165 2390 4.98 %
Rwork0.1754 45559 -
obs0.1775 47949 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.95 Å2
Refinement stepCycle: LAST / Resolution: 2→78.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4776 0 51 312 5139
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01275176
X-RAY DIFFRACTIONf_angle_d1.25687052
X-RAY DIFFRACTIONf_chiral_restr0.0615758
X-RAY DIFFRACTIONf_plane_restr0.0108954
X-RAY DIFFRACTIONf_dihedral_angle_d6.6769753
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.040.31441610.30132583X-RAY DIFFRACTION99.53
2.04-2.090.31281330.2512677X-RAY DIFFRACTION99.75
2.09-2.130.28851280.21812643X-RAY DIFFRACTION100
2.13-2.190.23421240.20012655X-RAY DIFFRACTION99.86
2.19-2.250.24111350.19012665X-RAY DIFFRACTION99.82
2.25-2.310.25931390.18692648X-RAY DIFFRACTION99.64
2.31-2.390.23051320.18192642X-RAY DIFFRACTION99.5
2.39-2.470.25321380.17482675X-RAY DIFFRACTION99.96
2.47-2.570.2151220.17242683X-RAY DIFFRACTION99.82
2.57-2.690.25581430.16922675X-RAY DIFFRACTION99.82
2.69-2.830.20421590.16562652X-RAY DIFFRACTION99.93
2.83-3.010.21451380.16982655X-RAY DIFFRACTION99.5
3.01-3.240.24891380.17412696X-RAY DIFFRACTION99.86
3.24-3.570.19271490.15652687X-RAY DIFFRACTION99.72
3.57-4.080.18511280.15222747X-RAY DIFFRACTION99.65
4.08-5.140.17651560.13992733X-RAY DIFFRACTION99.52
5.14-78.560.21391670.20992843X-RAY DIFFRACTION98.98
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)
15.960907339845.84572232792.392598376346.53661546082.384060590831.52619637772-0.003559740124080.0364585153642-0.3148388848350.04843206945680.143336993934-0.5135545098270.01789504716530.159544224688-0.1553736936930.1993501213240.0584797015436-0.01805903877880.222555543795-0.01779158926690.211225749471-17.84926673276.6210031283122.9445356543
21.387989844490.723488155564-0.00432077137313.13380672062-1.333835833391.72108071075-0.02591239059880.0318376978872-0.0284463428533-0.2277569190160.04579261437360.1242644620520.219359733891-0.130397457896-0.04574247238610.2655716266360.00581812958609-0.03597398933320.225951319857-0.006793142037340.196970714834-40.196008364-6.9323688924314.3090412436
32.412944686411.318904245520.5546656087553.17664924143-0.1797954760272.97525585498-0.1943741005640.350600456262-0.00432627840078-0.7692395123930.2320787526610.2189145807970.12199253744-0.122190590531-0.03525349728860.404538094424-0.0330203366288-0.04380706371590.2684881467050.005296668683120.182004198792-38.3668236713-6.344746977942.00946441508
43.127455803252.763539796190.6069541473113.571836787740.6646507196341.4090320467-0.2083674276040.391451903265-0.0826388282178-0.3846930236320.196270576945-0.2369679194840.1204176167920.1516916985850.01341500323210.2305244872730.05289743009210.02653767256930.2814975822370.008715439292460.18257613346-22.36264387852.320197801028.18930379925
54.29603673639-0.715685528803-0.1091020974712.026356061451.865093951646.79287811616-0.2665679889591.163699010520.241396032917-1.056771905040.462896870574-0.83112411736-0.6178017273580.865972829582-0.2003378584480.366500286426-0.09991264693940.05298224311570.5913084102410.0001122470973120.439310548355-12.476307022713.56810619984.22805916478
65.070365015210.4282198344631.883119290842.038561217981.591970358636.61800190427-0.09828702008651.10839245299-0.447334225163-0.4559248811280.0689052772116-1.169891313030.485575997710.9051723107720.05688104713530.498409480790.1512184532810.1015162513210.658501091731-0.07286676771880.679490590659-0.16289914132212.145938456713.6858769364
74.053926745253.240890131251.488305499386.668063657841.556388947743.103448357430.03700846379210.490732845356-0.2667777498250.04111913304480.236133494576-1.026601563130.1012890727190.383547806059-0.2916509815350.2423065773410.0959741448101-0.01120229142520.327854410533-0.0178038830880.447136439192-5.3967953700216.722897190719.9348677712
87.79443213434.97001060552.332149272483.956504821441.457347420621.205835226920.196552409608-0.1133034386760.3826007124270.380916159857-0.2018323250840.0462262418336-0.002970458872140.1047029476940.03514527756790.255412649090.0172312736227-0.03275925773750.204077698967-0.005724579019870.224489276095-17.491136830314.670623344232.3806344485
95.308925209392.06350533036-0.02426970849623.422636174220.5267847747952.968023123130.06252785637670.0209560833958-0.07082500525660.135681651448-0.134398551440.3378399239970.271252790092-0.2549300918950.04318447284370.2248200033830.0005215680978520.01149712348330.155296366052-0.02929926754830.197143611893-44.0460122079-10.08820983830.5864845795
102.794428861541.349709849151.349655470962.663340060740.427790769115.862960359770.0326782775442-0.466831784580.2069012979970.41312733915-0.1155958204040.315611489777-0.311654681448-0.4005171248180.07425536936450.3038299165570.003261719402460.05853627923690.24813557623-0.05104828564130.232202287331-39.53633545942.7244913081939.7117982301
113.459379716861.212020263710.641822525392.212078753640.456290652280.7919587790680.161692675519-0.3287645901420.1639979606610.559787510291-0.160430501141-0.229751593210.008984320470780.0248624816897-0.00600719737780.4076351278040.00580589081225-0.03189951373510.2732612528380.0110483685570.255931129771-21.89809638038.3485981277743.0257752271
126.981789064851.814882605461.808113879993.157359377230.3297605637912.873886303980.401062458674-0.451323289407-0.06738572879910.662951195497-0.321566834415-0.6306790401810.04648457099610.405081833055-0.04054110887710.420264461101-0.00865099164835-0.1381939372590.2832867702370.003251586287420.342052433075-10.233512989918.809037840442.5516942483
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 25 through 67 )AA25 - 671 - 43
22chain 'A' and (resid 68 through 102 )AA68 - 10244 - 78
33chain 'A' and (resid 103 through 152 )AA103 - 15279 - 128
44chain 'A' and (resid 153 through 241 )AA153 - 241129 - 217
55chain 'A' and (resid 242 through 266 )AA242 - 266218 - 242
66chain 'A' and (resid 267 through 290 )AA267 - 290243 - 266
77chain 'A' and (resid 291 through 328 )AA291 - 328267 - 304
88chain 'B' and (resid 17 through 67 )BF17 - 671 - 51
99chain 'B' and (resid 68 through 152 )BF68 - 15252 - 136
1010chain 'B' and (resid 153 through 205 )BF153 - 205137 - 189
1111chain 'B' and (resid 206 through 280 )BF206 - 280190 - 264
1212chain 'B' and (resid 281 through 332 )BF281 - 332265 - 316

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