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- PDB-3fhv: Structural basis of Salmonella typhi type IVb PilS and cystic fib... -

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Basic information

Entry
Database: PDB / ID: 3fhv
TitleStructural basis of Salmonella typhi type IVb PilS and cystic fibrosis transmembrane conductance regulator (CFTR) interaction
Components
  • Prepilin
  • cftr peptide
KeywordsCELL ADHESION/MEMBRANE PROTEIN / pils complex / cftr / CELL ADHESION-MEMBRANE PROTEIN COMPLEX
Function / homologyType 4 secretion system, PilS, N-terminal / PilS N terminal / TcpA-like pilin / TcpA-like pilin / Pilin-like / 2-Layer Sandwich / membrane / Alpha Beta / Pilus assembly protein PilX
Function and homology information
Biological speciesSalmonella typhi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBalakrishna, A.M. / Swaminathan, K.
CitationJournal: Proteins / Year: 2009
Title: Structural basis of typhoid: Salmonella typhi type IVb pilin (PilS) and cystic fibrosis transmembrane conductance regulator interaction.
Authors: Balakrishna, A.M. / Saxena, A.M. / Mok, H.Y. / Swaminathan, K.
History
DepositionDec 10, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Nov 1, 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 / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Prepilin
B: Prepilin
C: cftr peptide


Theoretical massNumber of molelcules
Total (without water)32,9393
Polymers32,9393
Non-polymers00
Water5,008278
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.799, 114.368, 31.772
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Prepilin / PilS


Mass: 15842.432 Da / Num. of mol.: 2 / Fragment: residues 26-181
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhi (bacteria) / Gene: pilS, STY4547, t4247 / Plasmid: Pet32a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: Q8Z1L1
#2: Protein/peptide cftr peptide


Mass: 1254.261 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. This sequence occurs naturally in humans.
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / Source method: isolated from a natural source / Formula: H2O
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: 2.15 Å3/Da / Density % sol: 42.67 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 4M Sodium Formate, VAPOR DIFFUSION, SITTING DROP, temperature 294'K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→8 Å / Num. obs: 27226 / % possible obs: 98.5 % / Redundancy: 7.2 % / Rsym value: 0.068 / Net I/σ(I): 26.4
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 6.12 / Rsym value: 0.12 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FHU

3fhu


Resolution: 1.9→8 Å / σ(F): 3 / σ(I): 3
RfactorNum. reflection% reflection
Rfree0.2485 2252 -
Rwork0.2067 --
all-27226 -
obs-20209 88.6 %
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2196 0 0 278 2474
LS refinement shellResolution: 1.8→1.86 Å
RfactorNum. reflection% reflection
Rfree0.2485 2252 -
Rwork0.2067 --
obs-20209 88.6 %

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