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- PDB-6w3t: Crystal structure of ligand-binding domain of Campylobacter jejun... -

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Basic information

Entry
Database: PDB / ID: 6w3t
TitleCrystal structure of ligand-binding domain of Campylobacter jejuni chemoreceptor Tlp3 in complex with L-norvaline
ComponentsMethyl-accepting chemotaxis protein
KeywordsSIGNALING PROTEIN / Bacterial chemotaxis / chemoreceptor / double Cache / ligand binding domain
Function / homology
Function and homology information


membrane => GO:0016020 / signal transduction / membrane
Similarity search - Function
Methyl-accepting chemotaxis protein-like, first PDC sensor domain / Double Cache domain 1 / Cache domain / Periplasmic sensor-like domain superfamily / 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).
Similarity search - Domain/homology
NORVALINE / Methyl-accepting chemotaxis protein / Methyl-accepting chemotaxis signal transduction protein
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKhan, M.F. / Machuca, M.A. / Rahman, M.M. / Roujeinikova, A.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: Biomolecules / Year: 2020
Title: Structure-Activity Relationship Study Reveals the Molecular Basis for Specific Sensing of Hydrophobic Amino Acids by theCampylobacter jejuniChemoreceptor Tlp3.
Authors: Khan, M.F. / Machuca, M.A. / Rahman, M.M. / Koc, C. / Norton, R.S. / Smith, B.J. / Roujeinikova, A.
History
DepositionMar 9, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2020Provider: repository / Type: Initial release
Revision 1.1May 27, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 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
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methyl-accepting chemotaxis protein
B: Methyl-accepting chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0128
Polymers57,4012
Non-polymers6116
Water6,251347
1
A: Methyl-accepting chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0064
Polymers28,7001
Non-polymers3053
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Methyl-accepting chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0064
Polymers28,7001
Non-polymers3053
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-36 kcal/mol
Surface area23350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.931, 137.770, 49.190
Angle α, β, γ (deg.)90.000, 93.920, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Methyl-accepting chemotaxis protein


Mass: 28700.498 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: D8X59_02240 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A3X8N4T9, UniProt: Q0P864*PLUS
#2: Chemical ChemComp-NVA / NORVALINE


Type: L-peptide linking / Mass: 117.146 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H11NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 347 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.47 Å3/Da / Density % sol: 50.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, sodium citrate and ammonium sulphate

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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 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.1→46.23 Å / Num. obs: 31594 / % possible obs: 97.6 % / Redundancy: 4.3 % / Biso Wilson estimate: 21.45 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 10.6
Reflection shellResolution: 2.1→2.16 Å / Rrim(I) all: 0.313

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4xmr

4xmr


Resolution: 2.1→39.969 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.25
RfactorNum. reflection% reflection
Rfree0.2042 1594 5.05 %
Rwork0.1589 --
obs0.1613 31561 97.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 89.65 Å2 / Biso mean: 25.2279 Å2 / Biso min: 4.37 Å2
Refinement stepCycle: final / Resolution: 2.1→39.969 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3871 0 38 348 4257
Biso mean--29.44 32.58 -
Num. residues----495
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064115
X-RAY DIFFRACTIONf_angle_d0.7945627
X-RAY DIFFRACTIONf_chiral_restr0.051662
X-RAY DIFFRACTIONf_plane_restr0.005728
X-RAY DIFFRACTIONf_dihedral_angle_d12.8831500
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1001-2.16780.28031540.202266497
2.1678-2.24530.25631500.1997269096
2.2453-2.33520.26481270.1847272397
2.3352-2.44150.27191360.1785271697
2.4415-2.57020.23721580.1738271097
2.5702-2.73120.21171440.17271397
2.7312-2.9420.24731430.1715274898
2.942-3.23790.20811350.1649277098
3.2379-3.70620.18141490.1418274998
3.7062-4.66820.15091340.1262276998

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