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- PDB-2fi7: Crystal Structure of PilF : Functional implication in the type 4 ... -

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Basic information

Entry
Database: PDB / ID: 2fi7
TitleCrystal Structure of PilF : Functional implication in the type 4 pilus biogenesis in Pseudomonas aeruginosa
Componentstype 4 fimbrial biogenesis protein PilF
KeywordsPROTEIN BINDING / PilF / TPR / Pseudomonas aeruginosa / Type 4 pilus
Function / homology
Function and homology information


type IV pilus assembly / type IV pilus-dependent motility / pilus assembly / TPR domain binding / secretion / cell outer membrane
Similarity search - Function
Pilus biogenesis/stability type IV, PilW / TPR repeat / Tetratricopeptide repeat / Tetratricopeptide repeat domain / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Prokaryotic membrane lipoprotein lipid attachment site profile. ...Pilus biogenesis/stability type IV, PilW / TPR repeat / Tetratricopeptide repeat / Tetratricopeptide repeat domain / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Prokaryotic membrane lipoprotein lipid attachment site profile. / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
: / Type IV pilus assembly protein PilF
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsKim, K.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2006
Title: Crystal structure of PilF: functional implication in the type 4 pilus biogenesis in Pseudomonas aeruginosa
Authors: Kim, K. / Oh, J. / Han, D. / Kim, E.E. / Lee, B. / Kim, Y.
History
DepositionDec 28, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: type 4 fimbrial biogenesis protein PilF
B: type 4 fimbrial biogenesis protein PilF


Theoretical massNumber of molelcules
Total (without water)60,1292
Polymers60,1292
Non-polymers00
Water3,945219
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)138.466, 68.239, 69.687
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly is a dimer.

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Components

#1: Protein type 4 fimbrial biogenesis protein PilF / Type IV pilus assembly protein pilF


Mass: 30064.697 Da / Num. of mol.: 2 / Fragment: Tetratricopeptide repeat motif
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)codonplus RIL / References: GenBank: 9949978, UniProt: Q9HXJ2*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 219 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.06 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 100mM Na-acetate (pH 4.6), 1.6M Na-formate, 100mM DTT, 15% Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 0.9796, 0.9797, 0.9719
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 13, 2004
RadiationMonochromator: GRAPHITE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97961
20.97971
30.97191
ReflectionResolution: 2.2→50 Å / Num. all: 45467 / Num. obs: 43694 / % possible obs: 96.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
Reflection shellResolution: 2.2→50 Å / % possible all: 96.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2.2→50 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.26 -Random
Rwork0.22 --
obs0.22 43694 -
all-45467 -
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3580 0 0 219 3799
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d1.092
X-RAY DIFFRACTIONc_bond_d0.0068

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