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- PDB-6s37: Ligand binding domain of the P. putida receptor PcaY_PP in comple... -

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Basic information

Entry
Database: PDB / ID: 6s37
TitleLigand binding domain of the P. putida receptor PcaY_PP in complex with salicylic acid
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
ACETATE ION / 2-HYDROXYBENZOIC ACID / Methyl-accepting chemotaxis protein PcaY
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 24, 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)119,2804
Polymers119,0832
Non-polymers1972
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-8 kcal/mol
Surface area12050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.842, 69.404, 93.540
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-SAL / 2-HYDROXYBENZOIC ACID / SALICYLIC ACID / Salicylic acid


Mass: 138.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
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: 1.8 Å3/Da / Density % sol: 33 %
Crystal growTemperature: 293 K / Method: counter-diffusion / pH: 6.5
Details: 30% PEG 8K, 0.1M Na Acetate, 0.1M Na-Cacodylate pH 6.50

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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 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→40.44 Å / Num. obs: 13404 / % possible obs: 98.97 % / Redundancy: 5.3 % / Biso Wilson estimate: 36.33 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.054 / Rrim(I) all: 0.127 / Net I/σ(I): 12.44
Reflection shellResolution: 2.3→2.382 Å / Redundancy: 5.1 % / Rmerge(I) obs: 1.14 / Mean I/σ(I) obs: 1.58 / Num. unique obs: 1321 / CC1/2: 0.627 / Rpim(I) all: 0.559 / Rrim(I) all: 1.27 / % possible all: 99.47

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Processing

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

6s18


Resolution: 2.3→40.44 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.64
RfactorNum. reflection% reflection
Rfree0.2545 681 5.08 %
Rwork0.1953 --
obs0.1981 13394 98.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→40.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2033 0 14 54 2101
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022404
X-RAY DIFFRACTIONf_angle_d0.4493275
X-RAY DIFFRACTIONf_dihedral_angle_d4.9441900
X-RAY DIFFRACTIONf_chiral_restr0.031354
X-RAY DIFFRACTIONf_plane_restr0.002465
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.47770.29891490.25322502X-RAY DIFFRACTION100
2.4777-2.7270.27021290.21672509X-RAY DIFFRACTION100
2.727-3.12150.28181380.21232531X-RAY DIFFRACTION100
3.1215-3.93250.23861270.17792493X-RAY DIFFRACTION97
3.9325-46.77960.23731380.1822678X-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)
13.1974-1.6041-0.08911.74251.10632.6007-0.18180.0681-0.32470.22060.3788-0.00780.38830.2291-0.24390.26730.0141-0.04070.2771-0.03860.230228.458445.737238.4834
24.2086-1.0071-0.20612.40181.43523.6149-0.10310.0112-0.31250.53280.5008-0.78180.55950.4484-0.33560.32230.0294-0.10280.3711-0.08860.393634.181147.606741.2335
33.6696-3.0521-0.27857.8930.24294.17370.02760.417-0.02630.01210.0181-1.6998-0.24150.99810.15880.2147-0.0330.05360.5201-0.03960.606337.824452.292633.1637
40.9948-0.93690.25272.231.08382.28880.12630.31680.0518-0.72460.0677-0.5192-0.02380.2223-0.13050.40980.1090.05140.5405-0.04830.383131.828543.323528.2679
52.51011.0425-0.62327.4649-1.17252.4015-0.03930.40330.0711-0.4515-0.0420.3530.06260.06730.05280.23690.0067-0.0280.33860.01360.19217.607350.69527.9552
63.65331.95460.15756.04930.25543.40560.003-0.1577-0.15280.2412-0.18620.20130.1571-0.11780.12910.18590.00570.0620.238-0.03390.198213.349548.705339.2648
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 28 through 62 )
2X-RAY DIFFRACTION2chain 'A' and (resid 63 through 96 )
3X-RAY DIFFRACTION3chain 'A' and (resid 97 through 128 )
4X-RAY DIFFRACTION4chain 'A' and (resid 129 through 166 )
5X-RAY DIFFRACTION5chain 'B' and (resid 33 through 92 )
6X-RAY DIFFRACTION6chain 'B' and (resid 93 through 158 )

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