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- PDB-6py4: Crystal structure of ligand-binding domain of Pseudomonas fluores... -

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Basic information

Entry
Database: PDB / ID: 6py4
TitleCrystal structure of ligand-binding domain of Pseudomonas fluorescens chemoreceptor CtaA in complex with L-leucine
ComponentsPutative methyl-accepting chemotaxis protein
KeywordsSIGNALING PROTEIN / Bacterial chemotaxis / chemoreceptor / double Cache / ligand binding domain
Function / homology
Function and homology information


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
LEUCINE / 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
DepositionJul 29, 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)27,1872
Polymers27,0551
Non-polymers1311
Water2,306128
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)70.210, 71.440, 112.770
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-433-

HOH

21A-452-

HOH

31A-458-

HOH

41A-465-

HOH

51A-520-

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-LEU / LEUCINE


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.83 Å3/Da / Density % sol: 56.52 %
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: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2→60.349 Å / Num. obs: 19503 / % possible obs: 99.8 % / Redundancy: 6.7 % / Rpim(I) all: 0.032 / Rrim(I) all: 0.083 / Rsym value: 0.076 / Net I/av σ(I): 6 / Net I/σ(I): 13.7 / Num. measured all: 131407
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
2-2.1170.3112.31959128170.1260.3360.3114.8100
2.11-2.246.90.2193.31848026610.0890.2360.2196.3100
2.24-2.396.90.1574.41733825130.0640.170.1578.3100
2.39-2.586.90.1235.31604023340.0510.1340.12310.2100
2.58-2.836.80.0927.21471521610.0380.10.09213.1100
2.83-3.166.70.06991323419730.0280.0750.06917.5100
3.16-3.656.60.05610.41150117330.0230.0610.05623100
3.65-4.476.10.0668.4918615020.0290.0720.06626.5100
4.47-6.326.20.0619.2733511790.0270.0670.06127.2100
6.32-33.2666.30.0341839876300.0150.0380.03428.493.9

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3C8C

3c8c


Resolution: 2→33.3 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.938 / SU B: 5.029 / SU ML: 0.132 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.156 / ESU R Free: 0.152
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2375 964 4.9 %RANDOM
Rwork0.1905 ---
obs0.1928 18531 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 135.92 Å2 / Biso mean: 40.122 Å2 / Biso min: 21.18 Å2
Baniso -1Baniso -2Baniso -3
1-7.21 Å20 Å20 Å2
2---2.38 Å20 Å2
3----4.83 Å2
Refinement stepCycle: final / Resolution: 2→33.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1676 0 9 128 1813
Biso mean--32.12 49.48 -
Num. residues----232
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.021725
X-RAY DIFFRACTIONr_bond_other_d0.0010.021635
X-RAY DIFFRACTIONr_angle_refined_deg1.5521.9692360
X-RAY DIFFRACTIONr_angle_other_deg0.84833744
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4255234
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.872455
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.41315256
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.371157
X-RAY DIFFRACTIONr_chiral_restr0.0940.2289
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211964
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02363
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 75 -
Rwork0.281 1347 -
all-1422 -
obs--99.93 %

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