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- PDB-6w3o: Crystal structure of ligand-binding domain of Campylobacter jejun... -

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Basic information

Entry
Database: PDB / ID: 6w3o
TitleCrystal structure of ligand-binding domain of Campylobacter jejuni chemoreceptor Tlp3 in complex with 4-methylisoleucine
ComponentsMethyl-accepting chemotaxis proteinMethyl-accepting chemotaxis proteins
KeywordsSIGNALING PROTEIN / Bacterial chemotaxis / chemoreceptor / double Cache / ligand binding domain
Function / homology
Function and homology information


chemotaxis / membrane => GO:0016020 / signal transduction / plasma membrane
Similarity search - Function
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
4-methylisoleucine / Methyl-accepting chemotaxis protein / Methyl-accepting chemotaxis signal transduction protein
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)57,98810
Polymers57,4012
Non-polymers5878
Water16,844935
1
A: Methyl-accepting chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0116
Polymers28,7001
Non-polymers3105
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Methyl-accepting chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9774
Polymers28,7001
Non-polymers2773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2640 Å2
ΔGint-77 kcal/mol
Surface area24130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.420, 137.720, 48.790
Angle α, β, γ (deg.)90.000, 94.040, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Methyl-accepting chemotaxis protein / Methyl-accepting chemotaxis proteins


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

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Non-polymers , 5 types, 943 molecules

#2: Chemical ChemComp-SKG / 4-methylisoleucine / 2~{S},3~{S})-2-azanyl-3,4-dimethyl-pentanoic acid


Type: L-peptide linking / Mass: 145.199 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H15NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 935 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.48 Å3/Da / Density % sol: 50.34 %
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: Feb 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.42→40.45 Å / Num. obs: 102980 / % possible obs: 98.5 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 17.1
Reflection shellResolution: 1.42→1.5 Å / Rmerge(I) obs: 0.147 / Mean I/σ(I) obs: 6.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
SCALAdata scaling
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4xmr

4xmr


Resolution: 1.42→40.45 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.741 / SU ML: 0.031 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.052 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1617 5124 5 %RANDOM
Rwork0.1146 ---
obs0.1169 97770 98.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 149.59 Å2 / Biso mean: 20.634 Å2 / Biso min: 6.08 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å2-0 Å20.43 Å2
2---0.64 Å20 Å2
3----0.16 Å2
Refinement stepCycle: final / Resolution: 1.42→40.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3926 0 34 935 4895
Biso mean--24.67 39.85 -
Num. residues----496
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.024269
X-RAY DIFFRACTIONr_bond_other_d0.0010.023903
X-RAY DIFFRACTIONr_angle_refined_deg1.4831.9735843
X-RAY DIFFRACTIONr_angle_other_deg1.03639129
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3145549
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.45825.99192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.6815749
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3211512
X-RAY DIFFRACTIONr_chiral_restr0.1060.2677
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.024825
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02804
X-RAY DIFFRACTIONr_rigid_bond_restr6.61238171
X-RAY DIFFRACTIONr_sphericity_free42.5855454
X-RAY DIFFRACTIONr_sphericity_bonded15.29858563
LS refinement shellResolution: 1.421→1.458 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.194 375 -
Rwork0.129 7104 -
all-7479 -
obs--96.89 %

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