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- PDB-6s18: Ligand binding domain of the P. putida receptor PcaY_PP in comple... -

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Basic information

Entry
Database: PDB / ID: 6s18
TitleLigand binding domain of the P. putida receptor PcaY_PP in complex with glycerol
ComponentsAromatic acid chemoreceptor
KeywordsSIGNALING PROTEIN / Ligand binding domain / Pseudomonas putida / chemotactic transducer / C6-ring carboxylic acids
Function / homology
Function and homology information


chemotaxis / transmembrane signaling receptor activity / signal transduction / plasma membrane
Similarity search - Function
Chemotaxis methyl-accepting receptor Tar-related, ligand-binding / Tar ligand binding domain homologue / 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). / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain
Similarity search - Domain/homology
Methyl-accepting chemotaxis protein PcaY
Similarity search - Component
Biological speciesPseudomonas putida KT2440 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.6 Å
AuthorsGavira, J.A. / Mantilla, M.A. / Fernandez, M. / Krell, T.
Funding support Spain, 2items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesBIO2016-76779-P Spain
Spanish Ministry of Science, Innovation, and UniversitiesBIO2016-74875-P Spain
CitationJournal: Febs J. / Year: 2021
Title: The structural basis for signal promiscuity in a bacterial chemoreceptor.
Authors: Gavira, J.A. / Matilla, M.A. / Fernandez, M. / Krell, T.
History
DepositionJun 18, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 21, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 4, 2020Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 1.3Apr 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aromatic acid chemoreceptor
B: Aromatic acid chemoreceptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,2114
Polymers119,0832
Non-polymers1282
Water3,693205
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: A, B
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint-28 kcal/mol
Surface area12660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.348, 67.768, 94.001
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 Aromatic acid chemoreceptor


Mass: 59541.609 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Ligand binding domain / Source: (gene. exp.) Pseudomonas putida KT2440 (bacteria) / Gene: pcaY, PP_2643 / Variant: ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q88JK6
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 205 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 44.4 %
Crystal growTemperature: 293 K / Method: counter-diffusion / pH: 6.5
Details: 30% PEG 8000, 0.1M Na Acetate, 0.1M Na-Cacodylate pH 6.50
Temp details: Incubator

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.6→47 Å / Num. obs: 38133 / % possible obs: 99.69 % / Redundancy: 4.6 % / Biso Wilson estimate: 24 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.024 / Rrim(I) all: 0.051 / Net I/σ(I): 17.86
Reflection shellResolution: 1.6→1.657 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.732 / Num. unique obs: 3766 / CC1/2: 0.605 / Rpim(I) all: 0.389 / Rrim(I) all: 0.833 / % possible all: 99.42

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
Aimlessdata scaling
Arcimboldophasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.6→47 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.33
RfactorNum. reflection% reflection
Rfree0.1908 1917 5.04 %
Rwork0.1645 --
obs0.1659 38052 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 36.3 Å2
Refinement stepCycle: LAST / Resolution: 1.6→47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2123 0 7 206 2336
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0182637
X-RAY DIFFRACTIONf_angle_d1.453608
X-RAY DIFFRACTIONf_dihedral_angle_d10.7062053
X-RAY DIFFRACTIONf_chiral_restr0.089391
X-RAY DIFFRACTIONf_plane_restr0.008512
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.25881200.23882569X-RAY DIFFRACTION100
1.64-1.68440.24311310.21262517X-RAY DIFFRACTION99
1.6844-1.73390.20681310.19412559X-RAY DIFFRACTION100
1.7339-1.78990.24321530.1842518X-RAY DIFFRACTION100
1.7899-1.85390.22611370.17292576X-RAY DIFFRACTION100
1.8539-1.92810.20641480.17092540X-RAY DIFFRACTION100
1.9281-2.01590.19651260.16152563X-RAY DIFFRACTION100
2.0159-2.12210.19641290.15732576X-RAY DIFFRACTION100
2.1221-2.25510.19311170.15072587X-RAY DIFFRACTION100
2.2551-2.42920.18711410.15772576X-RAY DIFFRACTION100
2.4292-2.67370.18881510.16022567X-RAY DIFFRACTION100
2.6737-3.06050.19681330.16812619X-RAY DIFFRACTION100
3.0605-3.85560.16821620.15042613X-RAY DIFFRACTION99
3.8556-47.0210.18761380.16862755X-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)
13.2564-2.62750.21326.56681.11012.53890.01210.0201-0.47830.21320.16140.15870.47090.2374-0.11490.16640.0306-0.0360.1968-0.00790.153228.923441.498338.6282
24.7161-3.6416-0.1298.84092.63313.41870.09260.1824-0.30260.18280.1755-0.31230.36050.306-0.19110.13260.0065-0.04420.1962-0.02950.16433.363847.667741.4268
34.9663-3.09870.70316.50381.37882.92070.08180.46740.2679-0.33940.1032-1.0871-0.18120.5908-0.110.187-0.05780.04080.39770.0150.342137.425851.496333.0701
41.7299-0.93640.15986.10981.34792.78250.12940.2838-0.0162-0.5489-0.0054-0.25190.07390.1597-0.10650.22930.0518-0.01410.3743-0.05110.217231.474540.155528.6175
52.2790.5845-0.22678.7666-0.85623.1013-0.02170.1689-0.3035-0.2841-0.06940.10350.42790.10680.07050.15820.01850.00130.1896-0.02610.126219.008242.641131.5264
62.28581.5006-1.77214.2458-3.14384.1662-0.130.31690.1308-0.51010.17920.44390.2815-0.1928-0.04730.2101-0.0087-0.05690.2628-0.0120.162714.683548.079926.58
72.75792.1823-0.88875.778-1.57343.9197-0.24620.0406-0.1231-0.37890.11360.08410.5013-0.29240.02340.1428-0.0070.02070.1911-0.02190.17869.872845.943737.8611
82.30640.0799-0.04782.5561-1.2743.19530.0651-0.1152-0.28890.2947-0.25950.04730.25250.18360.16710.16490.00910.0230.24260.03280.209317.298246.092242.5315
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 48 through 84 )
2X-RAY DIFFRACTION2chain 'A' and (resid 85 through 118 )
3X-RAY DIFFRACTION3chain 'A' and (resid 119 through 150 )
4X-RAY DIFFRACTION4chain 'A' and (resid 151 through 190 )
5X-RAY DIFFRACTION5chain 'B' and (resid 51 through 84 )
6X-RAY DIFFRACTION6chain 'B' and (resid 85 through 115 )
7X-RAY DIFFRACTION7chain 'B' and (resid 116 through 150 )
8X-RAY DIFFRACTION8chain 'B' and (resid 151 through 183 )

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