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- PDB-5t7m: LIGAND BINDING DOMAIN OF PSEUDOMONAS AERUGINOSA PAO1 AMINO ACID C... -

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Basic information

Entry
Database: PDB / ID: 5t7m
TitleLIGAND BINDING DOMAIN OF PSEUDOMONAS AERUGINOSA PAO1 AMINO ACID CHEMORECEPTOR PCTA IN COMPLEX WITH L-TRP
ComponentsChemotaxis protein
KeywordsSIGNALING PROTEIN / CHEMOTACTIC TRANSDUCER
Function / homology
Function and homology information


amino acid binding / response to amino acid / chemotaxis / transmembrane signaling receptor activity / signal transduction / plasma membrane
Similarity search - Function
Double Cache domain 1 / Cache domain / Periplasmic sensor-like domain superfamily / 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). / t-SNARE coiled-coil homology domain profile. / Target SNARE coiled-coil homology domain ...Double Cache domain 1 / Cache domain / Periplasmic sensor-like domain superfamily / 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). / t-SNARE coiled-coil homology domain profile. / Target SNARE coiled-coil homology domain / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain
Similarity search - Domain/homology
ACETATE ION / TRYPTOPHAN / Methyl-accepting chemotaxis protein PctA / Methyl-accepting chemotaxis protein PctA
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsGavira, J.A. / Rico-Jimenez, M. / Ortega, A. / Conejero-Muriel, M. / Zhulin, I. / Krell, T.
Funding support Spain, 1items
OrganizationGrant numberCountry
MICINNBIO2013-4297-P Spain
Citation
Journal: Mbio / Year: 2020
Title: How Bacterial Chemoreceptors Evolve Novel Ligand Specificities
Authors: Gavira, J.A. / Jimenez-Rico, M. / Pineda-Molina, E. / Krell, T.
#1: Journal: Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun.
Year: 2013
Title: Purification, crystallization and preliminary crystallographic analysis of the ligand-binding regions of the PctA and PctB chemoreceptors from Pseudomonas aeruginosa in complex with amino acids.
Authors: Rico-Jimenez, M. / Munoz-Martinez, F. / Krell, T. / Gavira, J.A. / Pineda-Molina, E.
History
DepositionSep 5, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2018Group: Data collection / Database references / Structure summary
Category: audit_author / citation / struct / Item: _citation.title / _struct.title
Revision 1.2Jan 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name
Revision 1.3Jan 17, 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: Chemotaxis protein
B: Chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5558
Polymers58,9472
Non-polymers6096
Water3,945219
1
A: Chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7964
Polymers29,4731
Non-polymers3223
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7604
Polymers29,4731
Non-polymers2863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.110, 78.410, 116.450
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 Chemotaxis protein / Methyl-accepting chemotaxis protein PctA / Uncharacterized protein


Mass: 29473.318 Da / Num. of mol.: 2 / Fragment: LIGAND BINDING DOMAIN, RESIDUES 1-270
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: pctA_1, mcpB_2, AO946_32780, AOY09_01348, PAERUG_P32_London_17_VIM_2_10_11_00198
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H0Z019, UniProt: G3XD24*PLUS
#2: Chemical ChemComp-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H12N2O2
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsL-TRYPTOPHAN (TRP): NATURAL LIGAND

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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: 3.6 Å3/Da / Density % sol: 66 %
Crystal growTemperature: 293 K / Method: liquid diffusion / pH: 4.6
Details: COUNTERDIFFUSION METHOD: 2.0 M SODIUM FORMATE, 0.1 M NA ACT pH 4.6
PH range: 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.25→58.225 Å / Num. obs: 32028 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 8.2 % / Biso Wilson estimate: 40.24 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.9
Reflection shellResolution: 2.25→2.32 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2 / CC1/2: 0.791 / % possible all: 100

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Processing

Software
NameClassification
XDSdata reduction
SCALAdata scaling
PHASERphasing
PHENIXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5T65

5t65


Resolution: 2.25→58.225 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 23.95
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1620 5.1 %Ramdon
Rwork0.1852 ---
obs0.1876 31994 99.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 49.4 Å2
Refinement stepCycle: LAST / Resolution: 2.25→58.225 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3634 0 43 219 3896
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083926
X-RAY DIFFRACTIONf_angle_d1.1615366
X-RAY DIFFRACTIONf_dihedral_angle_d13.6521443
X-RAY DIFFRACTIONf_chiral_restr0.046616
X-RAY DIFFRACTIONf_plane_restr0.005695
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.31620.32291360.26132489X-RAY DIFFRACTION100
2.3162-2.3910.26511400.23712478X-RAY DIFFRACTION100
2.391-2.47650.28151270.24342512X-RAY DIFFRACTION100
2.4765-2.57560.31431540.22772467X-RAY DIFFRACTION100
2.5756-2.69280.27971360.22132496X-RAY DIFFRACTION100
2.6928-2.83480.30371390.21772501X-RAY DIFFRACTION100
2.8348-3.01240.24541140.21562533X-RAY DIFFRACTION100
3.0124-3.2450.25941310.20862534X-RAY DIFFRACTION100
3.245-3.57150.25151380.18782539X-RAY DIFFRACTION100
3.5715-4.08820.22411460.16942536X-RAY DIFFRACTION100
4.0882-5.15020.19131390.14082580X-RAY DIFFRACTION100
5.1502-58.24450.17231200.15782709X-RAY DIFFRACTION99

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