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- PDB-4noa: Truncated minor pilin PilE from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 4noa
TitleTruncated minor pilin PilE from Pseudomonas aeruginosa
ComponentsType 4 fimbrial biogenesis protein PilE
KeywordsUNKNOWN FUNCTION
Function / homology
Function and homology information


type IV pilus assembly / type IV pilus-dependent motility / pilus assembly / membrane => GO:0016020 / plasma membrane
Similarity search - Function
Type IV pilus non-core minor pilin PilE-like / Type IV minor pilin ComP, DNA uptake sequence receptor / Prokaryotic N-terminal methylation site. / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site
Similarity search - Domain/homology
Type IV pilus non-core minor pilin PilE
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.25 Å
AuthorsNguyen, Y. / Sugiman-Marangos, S.N. / Bell, S. / Junop, M.S. / Burrows, L.L.
CitationJournal: To be Published
Title: Crystal structure of truncated minor pilin PilE from Pseudomonas aeruginosa
Authors: Nguyen, Y. / Sugiman-Marangos, S.N. / Bell, S. / Harvey, H. / Junop, M.S. / Burrows, L.L.
History
DepositionNov 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Type 4 fimbrial biogenesis protein PilE


Theoretical massNumber of molelcules
Total (without water)12,0931
Polymers12,0931
Non-polymers00
Water4,396244
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.159, 35.560, 43.536
Angle α, β, γ (deg.)90.00, 97.33, 90.00
Int Tables number5
Space group name H-MC121
DetailsAUTHORS STATE THAT THE BIOLOGICAL ASSEMBLY IN UNKNOWN.

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Components

#1: Protein Type 4 fimbrial biogenesis protein PilE


Mass: 12093.130 Da / Num. of mol.: 1 / Fragment: UNP residues 36-141
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: PA4556, pilE / Plasmid: pET151-D-topo / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B(DE3) / References: UniProt: G3XD43
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 244 / Source method: isolated from a natural source / Formula: H2O

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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: 2.42 Å3/Da / Density % sol: 49.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2 M Ammonium tartrate dibasic, 20% (w/v) PEG 3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.979 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 25, 2012 / Details: Mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.25→50 Å / Num. all: 30749 / Num. obs: 30749 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 8.28 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 20.7
Reflection shellResolution: 1.25→1.27 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 7.6 / Num. unique all: 1462 / Rsym value: 0.21 / % possible all: 89.6

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Processing

Software
NameVersionClassification
CBASSdata collection
PHENIX(phenix.autosol)model building
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.25→43.181 Å / SU ML: 0.12 / σ(F): 0 / Phase error: 14.68 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.1753 1996 6.51 %Random
Rwork0.159 ---
obs0.1601 30645 94.82 %-
all-30645 --
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.969 Å2 / ksol: 0.442 e/Å3
Displacement parametersBiso mean: 11.51 Å2
Baniso -1Baniso -2Baniso -3
1-1.1712 Å20 Å21.8603 Å2
2--1.2334 Å2-0 Å2
3----2.4046 Å2
Refinement stepCycle: LAST / Resolution: 1.25→43.181 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms810 0 0 244 1054
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005850
X-RAY DIFFRACTIONf_angle_d0.9651166
X-RAY DIFFRACTIONf_dihedral_angle_d10.136320
X-RAY DIFFRACTIONf_chiral_restr0.063136
X-RAY DIFFRACTIONf_plane_restr0.004156
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.27970.19611310.18651873X-RAY DIFFRACTION87
1.2797-1.31430.18021400.1781993X-RAY DIFFRACTION92
1.3143-1.3530.1811370.16371952X-RAY DIFFRACTION92
1.353-1.39670.18391400.16432002X-RAY DIFFRACTION94
1.3967-1.44660.16081400.14932015X-RAY DIFFRACTION94
1.4466-1.50450.18021390.14452012X-RAY DIFFRACTION94
1.5045-1.5730.15941410.14212015X-RAY DIFFRACTION95
1.573-1.65590.15341430.13582054X-RAY DIFFRACTION95
1.6559-1.75970.17111450.1452080X-RAY DIFFRACTION96
1.7597-1.89560.19461450.15772089X-RAY DIFFRACTION97
1.8956-2.08630.18541450.16092082X-RAY DIFFRACTION97
2.0863-2.38820.17651470.15562106X-RAY DIFFRACTION98
2.3882-3.00880.17421510.1682165X-RAY DIFFRACTION98
3.0088-43.20650.17031520.16472211X-RAY DIFFRACTION99

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