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- PDB-6py3: Crystal structure of ligand-binding domain of Pseudomonas fluores... -

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Basic information

Entry
Database: PDB / ID: 6py3
TitleCrystal structure of ligand-binding domain of Pseudomonas fluorescens chemoreceptor CtaA in complex with L-isoleucine
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
Similarity search - Domain/homology
ISOLEUCINE / Putative methyl-accepting chemotaxis protein
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 28, 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
B: Putative methyl-accepting chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3734
Polymers54,1112
Non-polymers2622
Water5,206289
1
A: Putative methyl-accepting chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1872
Polymers27,0551
Non-polymers1311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative methyl-accepting chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1872
Polymers27,0551
Non-polymers1311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)133.050, 70.700, 70.990
Angle α, β, γ (deg.)90.000, 122.100, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-427-

HOH

21B-523-

HOH

31B-535-

HOH

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Components

#1: Protein Putative methyl-accepting chemotaxis protein


Mass: 27055.496 Da / Num. of mol.: 2
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-ILE / ISOLEUCINE


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C6H13NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / 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: 2.68 Å3/Da / Density % sol: 55.43 %
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: Nov 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.557
11H+4/2L, -K, -L20.443
ReflectionResolution: 1.9→60.137 Å / Num. obs: 42486 / % possible obs: 96.7 % / Redundancy: 3.9 % / Rpim(I) all: 0.031 / Rrim(I) all: 0.061 / Rsym value: 0.053 / Net I/av σ(I): 12 / Net I/σ(I): 16.5 / Num. measured all: 164140
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
1.9-23.90.3062.52385061310.1790.3550.3064.496.1
2-2.123.90.2063.72260758110.120.2380.2066.496.3
2.12-2.273.90.1455.32136955000.0850.1680.1458.796.5
2.27-2.453.90.1017.61991051310.0590.1170.10111.596.7
2.45-2.693.90.0799.51832347290.0460.0910.07914.197.1
2.69-33.90.05613.21662742980.0330.0650.05618.697.2
3-3.473.90.03519.41461437900.0210.0410.03528.397.2
3.47-4.253.80.02722.51230532140.0160.0310.02737.497.2
4.25-6.013.80.02423.5954125150.0140.0280.02441.397
6.01-37.4743.70.02222.3499413670.0140.0260.02239.594.6

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Processing

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

3c8c


Resolution: 1.9→37.47 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.803 / SU ML: 0.087 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.029 / ESU R Free: 0.028 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2248 2027 4.8 %RANDOM
Rwork0.1806 ---
obs0.1827 40456 95.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 146.05 Å2 / Biso mean: 28.293 Å2 / Biso min: 12.96 Å2
Baniso -1Baniso -2Baniso -3
1--25.9 Å20 Å2-1.25 Å2
2--41.27 Å20 Å2
3----15.37 Å2
Refinement stepCycle: final / Resolution: 1.9→37.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3463 0 18 289 3770
Biso mean--18.84 35.32 -
Num. residues----472
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.023559
X-RAY DIFFRACTIONr_bond_other_d0.0010.023339
X-RAY DIFFRACTIONr_angle_refined_deg1.461.9684859
X-RAY DIFFRACTIONr_angle_other_deg0.79737677
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1635472
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.93125.078128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.87115547
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0091512
X-RAY DIFFRACTIONr_chiral_restr0.0980.2584
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0214053
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02733
LS refinement shellResolution: 1.9→1.945 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.247 151 -
Rwork0.206 2684 -
obs--87.31 %

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