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- PDB-6w3p: Crystal structure of ligand-binding domain of Campylobacter jejun... -

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Basic information

Entry
Database: PDB / ID: 6w3p
TitleCrystal structure of ligand-binding domain of Campylobacter jejuni chemoreceptor Tlp3 in complex with beta-methylnorleucine
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
beta-methylnorleucine / Methyl-accepting chemotaxis protein / Methyl-accepting chemotaxis signal transduction protein
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.383 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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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)58,19914
Polymers57,4012
Non-polymers79812
Water15,187843
1
A: Methyl-accepting chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1518
Polymers28,7001
Non-polymers4507
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Methyl-accepting chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0486
Polymers28,7001
Non-polymers3485
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-110 kcal/mol
Surface area24430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.110, 138.110, 48.790
Angle α, β, γ (deg.)90.000, 94.720, 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


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 , 6 types, 855 molecules

#2: Chemical ChemComp-SKJ / beta-methylnorleucine / (2~{S},3~{R})-2-azanyl-3-methyl-hexanoic 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


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


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 843 / 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: 2.46 Å3/Da / Density % sol: 50.07 %
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: 1.38→35.86 Å / Num. obs: 100314 / % possible obs: 89.1 % / Redundancy: 3.1 % / Biso Wilson estimate: 13.98 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 10.1
Reflection shellResolution: 1.38→1.46 Å / Rmerge(I) obs: 0.333 / Mean I/σ(I) obs: 2.8

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Processing

Software
NameVersionClassification
SCALAdata scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4xmr

4xmr


Resolution: 1.383→33.43 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.66
RfactorNum. reflection% reflection
Rfree0.1872 5026 5.02 %
Rwork0.1376 --
obs0.1401 100208 88.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 156.6 Å2 / Biso mean: 25.2077 Å2 / Biso min: 6.88 Å2
Refinement stepCycle: final / Resolution: 1.383→33.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3923 0 43 843 4809
Biso mean--29.64 41.61 -
Num. residues----495
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124302
X-RAY DIFFRACTIONf_angle_d1.3515886
X-RAY DIFFRACTIONf_chiral_restr0.105677
X-RAY DIFFRACTIONf_plane_restr0.018770
X-RAY DIFFRACTIONf_dihedral_angle_d14.4941632
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.383-1.39870.2351860.1837304785
1.3987-1.41520.2591680.1883312889
1.4152-1.43240.2731850.1856314488
1.4324-1.45060.22551600.1791309587
1.4506-1.46970.24511560.1648314788
1.4697-1.48980.21961600.1529309687
1.4898-1.51110.20571440.1475312587
1.5111-1.53360.21551530.1409311587
1.5336-1.55760.19941550.1436305385
1.5576-1.58310.20761580.1373315588
1.5831-1.61040.19421550.136303686
1.6104-1.63970.1921580.1291306286
1.6397-1.67120.19171760.1177302485
1.6712-1.70540.18151630.1161304885
1.7054-1.74240.18981660.1146303685
1.7424-1.7830.18671720.1194299785
1.783-1.82750.17991560.1302301684
1.8275-1.8770.18251500.1258308286
1.877-1.93220.20721440.1241301385
1.9322-1.99450.17141560.1183306585
1.9945-2.06580.16831940.1218304687
2.0658-2.14850.16921580.1219316089
2.1485-2.24630.19211820.1246324591
2.2463-2.36470.1721660.1241339794
2.3647-2.51280.19711810.1354347897
2.5128-2.70670.17181880.1421355699
2.7067-2.9790.18861920.14563564100
2.979-3.40960.19931810.13773570100
3.4096-4.29440.17851920.1356350197

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