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- PDB-6q0g: Crystal structure of ligand-binding domain of Pseudomonas fluores... -

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Basic information

Entry
Database: PDB / ID: 6q0g
TitleCrystal structure of ligand-binding domain of Pseudomonas fluorescens chemoreceptor CtaA in complex with L-proline
ComponentsPutative methyl-accepting chemotaxis protein
KeywordsSIGNALING PROTEIN / Bacterial chemotaxis / chemoreceptor / double Cache / ligand binding domain
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). / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) 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). / 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
PROLINE / Putative methyl-accepting chemotaxis protein
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsUd-Din, I.A. / Khan, M.F. / Roujeinikova, A.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: Mol.Plant Microbe Interact. / Year: 2020
Title: Broad Specificity of Amino Acid Chemoreceptor CtaA ofPseudomonas fluorescensIs Afforded by Plasticity of Its Amphipathic Ligand-Binding Pocket.
Authors: Ud-Din, A.I.M.S. / Khan, M.F. / Roujeinikova, A.
History
DepositionAug 1, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 2023Group: 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: Putative methyl-accepting chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2424
Polymers27,0551
Non-polymers1863
Water3,477193
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.730, 71.770, 112.320
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-513-

HOH

21A-524-

HOH

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Components

#1: Protein Putative methyl-accepting chemotaxis protein


Mass: 27055.496 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (strain Pf0-1) (bacteria)
Strain: Pf0-1 / Gene: Pfl01_4431 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q3K7T6
#2: Chemical ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.3 Å3/Da / Density % sol: 46.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: Ammonium sulfate and Tris-HCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→60.478 Å / Num. obs: 17230 / % possible obs: 100 % / Redundancy: 6.9 % / Biso Wilson estimate: 27.55 Å2 / Rpim(I) all: 0.038 / Rrim(I) all: 0.1 / Rsym value: 0.092 / Net I/av σ(I): 4.4 / Net I/σ(I): 11.7 / Num. measured all: 118988
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2-2.1170.37621740924710.1510.4060.3764.4100
2.11-2.2470.2762.71652423510.1110.2980.2765.7100
2.24-2.3970.1943.41542922020.0790.210.1947.4100
2.39-2.5870.16141449920670.0650.1740.1618.7100
2.58-2.8370.12251335719160.0490.1320.12211.4100
2.83-3.166.90.0925.91197917250.0380.10.09215100
3.16-3.656.90.0776.61060515470.0310.0830.07719.3100
3.65-4.476.80.0687.9884813100.0280.0740.06822100
4.47-6.326.60.0717.1682610400.0290.0770.07122100
6.32-35.9535.80.0647.535126010.0290.0710.06421.499.1

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
SCALA3.3.22data scaling
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3C8C

3c8c


Resolution: 2→35.953 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2603 830 4.83 %
Rwork0.1996 16353 -
obs0.2026 17183 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 95.45 Å2 / Biso mean: 39.4568 Å2 / Biso min: 14.87 Å2
Refinement stepCycle: final / Resolution: 2→35.953 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1607 0 10 193 1810
Biso mean--31.77 48.23 -
Num. residues----221
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111646
X-RAY DIFFRACTIONf_angle_d1.1552248
X-RAY DIFFRACTIONf_chiral_restr0.063270
X-RAY DIFFRACTIONf_plane_restr0.008288
X-RAY DIFFRACTIONf_dihedral_angle_d4.004979
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2-2.12550.28381260.22112679
2.1255-2.28960.26631360.20962695
2.2896-2.51990.23521430.21192677
2.5199-2.88440.29111350.23232722
2.8844-3.63350.30521550.19922725

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