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- PDB-3soj: Francisella tularensis pilin PilE -

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Basic information

Entry
Database: PDB / ID: 3soj
TitleFrancisella tularensis pilin PilE
ComponentsPilE
KeywordsCELL ADHESION / pilus subunit / extracellular
Function / homologyGlycoprotein, Type 4 Pilin / Glycoprotein, Type 4 Pilin / Prokaryotic N-terminal methylation site. / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / 2-Layer Sandwich / Alpha Beta / Type IV pili fiber building block protein
Function and homology information
Biological speciesFrancisella tularensis subsp. tularensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1 Å
AuthorsWood, T. / Arvai, A.S. / Shin, D.S. / Hartung, S. / Kolappan, S. / Craig, L. / Tainer, J.A.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Ultrahigh Resolution and Full-length Pilin Structures with Insights for Filament Assembly, Pathogenic Functions, and Vaccine Potential.
Authors: Hartung, S. / Arvai, A.S. / Wood, T. / Kolappan, S. / Shin, D.S. / Craig, L. / Tainer, J.A.
History
DepositionJun 30, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2012Group: Database references
Revision 1.2May 14, 2014Group: Refinement description

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PilE
B: PilE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4553
Polymers24,3592
Non-polymers961
Water5,693316
1
A: PilE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2752
Polymers12,1791
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PilE


Theoretical massNumber of molelcules
Total (without water)12,1791
Polymers12,1791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.887, 62.160, 82.615
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PilE / Type IV pili fiber building block protein


Mass: 12179.265 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. tularensis (bacteria)
Strain: SCHU S4 / Gene: FTT0889c, FTT_0889c, pilE2 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): Escherichia coli Origami2 (DE3) / References: UniProt: Q5NGF6
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 316 / 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: 1.79 Å3/Da / Density % sol: 31.13 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 38% PEG 2000 MME 5% saturated LiSO4 25mM Bis-Tris propane 20mM Xylitol 10mM DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL9-111.0, 0.9
SSRL BL9-12
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 9, 2007
RadiationMonochromator: Side-scattering cuberoot I-beam bent single crystal
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.91
ReflectionResolution: 1→34.4 Å / Num. all: 95136 / Num. obs: 94896 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellHighest resolution: 1 Å / % possible all: 100

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Processing

Software
NameClassification
HKL-2000data collection
SHELXSphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1→34.4 Å / SU ML: 0.18 / σ(F): 1.34 / Phase error: 16.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1813 4745 5 %Random 10%
Rwork0.1597 ---
all0.1608 95136 --
obs0.1608 94891 99.78 %-
Solvent computationShrinkage radii: 0.65 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.543 Å2 / ksol: 0.412 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.5109 Å2-0 Å20 Å2
2---0.4315 Å2-0 Å2
3---0.9425 Å2
Refinement stepCycle: LAST / Resolution: 1→34.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1698 0 5 316 2019
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012033
X-RAY DIFFRACTIONf_angle_d1.3662809
X-RAY DIFFRACTIONf_dihedral_angle_d11.902730
X-RAY DIFFRACTIONf_chiral_restr0.08345
X-RAY DIFFRACTIONf_plane_restr0.008379
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1-1.0110.33411350.32622779X-RAY DIFFRACTION94
1.011-1.02290.25731680.25652967X-RAY DIFFRACTION99
1.0229-1.03540.26911600.22592956X-RAY DIFFRACTION100
1.0354-1.04850.21571580.20752955X-RAY DIFFRACTION100
1.0485-1.06230.2021600.18272970X-RAY DIFFRACTION100
1.0623-1.07680.19471720.16512975X-RAY DIFFRACTION100
1.0768-1.09220.21191450.1553013X-RAY DIFFRACTION100
1.0922-1.10850.16261620.14832970X-RAY DIFFRACTION100
1.1085-1.12580.17761580.14472975X-RAY DIFFRACTION100
1.1258-1.14430.19371650.14332955X-RAY DIFFRACTION100
1.1443-1.1640.20381670.13832996X-RAY DIFFRACTION100
1.164-1.18520.16781490.14092958X-RAY DIFFRACTION100
1.1852-1.2080.15681340.143035X-RAY DIFFRACTION100
1.208-1.23260.17431670.14012969X-RAY DIFFRACTION100
1.2326-1.25940.16041660.14273007X-RAY DIFFRACTION100
1.2594-1.28870.17871570.14122982X-RAY DIFFRACTION100
1.2887-1.3210.18011660.14282977X-RAY DIFFRACTION100
1.321-1.35670.16441630.14063036X-RAY DIFFRACTION100
1.3567-1.39660.17371590.13512971X-RAY DIFFRACTION100
1.3966-1.44170.18881680.14642982X-RAY DIFFRACTION100
1.4417-1.49320.18481400.14453037X-RAY DIFFRACTION100
1.4932-1.5530.18011750.14062998X-RAY DIFFRACTION100
1.553-1.62370.1741570.14453044X-RAY DIFFRACTION100
1.6237-1.70930.17621520.1523005X-RAY DIFFRACTION100
1.7093-1.81640.19291590.15933056X-RAY DIFFRACTION100
1.8164-1.95660.17471450.15853044X-RAY DIFFRACTION100
1.9566-2.15350.17321530.15763074X-RAY DIFFRACTION100
2.1535-2.4650.17551710.15713053X-RAY DIFFRACTION100
2.465-3.10530.18851490.17823141X-RAY DIFFRACTION100
3.1053-34.42410.1761650.1673266X-RAY DIFFRACTION100

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