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- PDB-3fhu: Crystal structure of type IV b pilin from Salmonella typhi -

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Basic information

Entry
Database: PDB / ID: 3fhu
TitleCrystal structure of type IV b pilin from Salmonella typhi
ComponentsPrepilin
KeywordsCELL ADHESION / pilin
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 / MAD / Resolution: 2.1 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 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 9, 2020Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.4Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Prepilin
B: Prepilin


Theoretical massNumber of molelcules
Total (without water)31,6852
Polymers31,6852
Non-polymers00
Water3,927218
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.880, 114.530, 31.750
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.23 Å3/Da / Density % sol: 44.95 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 4M Sodium Formate, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.97939, 0.97978, 0.95
DetectorType: Brandeis B4 / Detector: CCD / Date: Oct 9, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979391
20.979781
30.951
ReflectionResolution: 2.1→8 Å / Num. all: 22854 / Num. obs: 21898 / % possible obs: 95.8 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 1 / Redundancy: 4.3 % / Rsym value: 0.029 / Net I/σ(I): 26.5
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 7.39 / Num. unique all: 23297 / Rsym value: 0.15

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Processing

Software
NameClassification
SnBphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.1→8 Å / σ(F): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.26 2198 -
Rwork0.22 --
all-22854 -
obs-21898 95.8 %
Refinement stepCycle: LAST / Resolution: 2.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2108 0 0 218 2326
LS refinement shellResolution: 2.1→2.18 Å
RfactorNum. reflection% reflection
Rfree0.2639 2198 -
Rwork0.2278 --
obs-21898 95.8 %

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