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- PDB-6s1a: Ligand binding domain of the P. putida receptor PcaY_PP -

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Basic information

Entry
Database: PDB / ID: 6s1a
TitleLigand binding domain of the P. putida receptor PcaY_PP
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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.112 Å
AuthorsGavira, J.A. / Matilla, 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 1.4Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)119,1793
Polymers119,0832
Non-polymers961
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-24 kcal/mol
Surface area12910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.519, 69.228, 90.805
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 (strain ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440) (bacteria)
Strain: ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440 / Gene: pcaY, PP_2643
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q88JK6
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 1.84 Å3/Da / Density % sol: 33.2 %
Crystal growTemperature: 293.5 K / Method: counter-diffusion / pH: 8.5 / Details: 2.0M NH4 Sulphate,0.1M Tris-HCl pH 8.50

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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: Nov 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.11→38.51 Å / Num. obs: 14061 / % possible obs: 88 % / Redundancy: 4 % / Biso Wilson estimate: 34.73 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rrim(I) all: 0.07 / Net I/σ(I): 12.68
Reflection shellResolution: 2.11→2.19 Å / Redundancy: 4 % / Rmerge(I) obs: 0.473 / Mean I/σ(I) obs: 2.63 / Num. unique obs: 1487 / CC1/2: 0.841 / Rrim(I) all: 0.54 / % possible all: 96

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6S18

6s18


Resolution: 2.112→38.507 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.63
RfactorNum. reflection% reflection
Rfree0.2603 706 5.02 %
Rwork0.212 --
obs0.2145 14053 88.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 41.83 Å2
Refinement stepCycle: LAST / Resolution: 2.112→38.507 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2140 0 5 80 2225
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042578
X-RAY DIFFRACTIONf_angle_d0.5783516
X-RAY DIFFRACTIONf_dihedral_angle_d7.9112244
X-RAY DIFFRACTIONf_chiral_restr0.034375
X-RAY DIFFRACTIONf_plane_restr0.003503
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1119-2.2750.34021280.24682504X-RAY DIFFRACTION85
2.275-2.50390.3011480.23082922X-RAY DIFFRACTION98
2.5039-2.86610.27561300.22452439X-RAY DIFFRACTION81
2.8661-3.61050.26791460.21332719X-RAY DIFFRACTION90
3.6105-38.51310.2321540.19682763X-RAY DIFFRACTION87
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)
11.07760.22520.85177.4977-2.09881.67940.0688-0.0177-0.0045-0.0331-0.1422-0.1873-0.010.12760.05240.23840.0330.0870.29280.00030.242311.967648.219137.2564
21.356-0.9978-0.30863.40141.5141.2589-0.1265-0.1415-0.00710.29320.1525-0.01990.0817-0.0034-0.04080.2421-0.01550.00090.2860.00530.209827.977248.575739.9813
30.6691-0.38730.35837.8994-1.02021.88860.00960.1620.20240.1218-0.1418-0.2684-0.11660.09530.13450.1844-0.00320.00770.27110.00780.252233.494447.147730.5584
42.16661.5746-0.246.7574-1.42371.867-0.01070.0494-0.2139-0.1104-0.05210.03450.15430.00540.03030.17620.00820.0090.2284-0.01210.146914.853545.192227.4791
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 119 through 186 )
2X-RAY DIFFRACTION2chain 'A' and (resid 49 through 115 )
3X-RAY DIFFRACTION3chain 'A' and (resid 116 through 188 )
4X-RAY DIFFRACTION4chain 'B' and (resid 49 through 118 )

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