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- PDB-2ho1: Functional Characterization of Pseudomonas Aeruginosa pilF -

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Basic information

Entry
Database: PDB / ID: 2ho1
TitleFunctional Characterization of Pseudomonas Aeruginosa pilF
ComponentsType 4 fimbrial biogenesis protein PilF
KeywordsPROTEIN BINDING / pilF / Type IV pilus biogenesis / Pseudomonas aeruginosa / TPR / superhelix
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 / SAD / Resolution: 2 Å
AuthorsKoo, J.
CitationJournal: J.Bacteriol. / Year: 2008
Title: PilF is an outer membrane lipoprotein required for multimerization and localization of the Pseudomonas aeruginosa Type IV pilus secretin.
Authors: Koo, J. / Tammam, S. / Ku, S.Y. / Sampaleanu, L.M. / Burrows, L.L. / Howell, P.L.
History
DepositionJul 13, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 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 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Remark 300BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAINS. ...BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAINS. THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)58,0092
Polymers58,0092
Non-polymers00
Water5,621312
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)137.099, 69.047, 70.126
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-273-

HOH

DetailsThe asymmetric unit contains two pilF monomers. The biological functional unit is unknown.

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Components

#1: Protein Type 4 fimbrial biogenesis protein PilF


Mass: 29004.740 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: pilF / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: Q9HXJ2
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 2.87 Å3/Da / Density % sol: 57.13 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.095 mM Sodium-citrate pH 5.6, 19% isopropanol (v/v), 19% PEG 4K (w/v), 5% glycerol (v/v), VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.980301, 0.95
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 17, 2006
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9803011
20.951
Reflection

D res high: 2 Å

Redundancy (%)IDAv σ(I) over netINumberRmerge(I) obsΧ2D res low (Å)Num. obs% possible obs
6.95110.93202170.0620.9530.854571799.6
7.04210.73254120.0610.9828.264590099.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancyRejects
4.3130.8599.610.040.696.69183
3.424.319910.040.626.6742
2.993.4299.710.0580.687.09136
2.712.9910010.0950.787.25226
2.522.7110010.1430.97.28264
2.372.5210010.2121.027.3273
2.252.3710010.2831.127.29302
2.152.2510010.3641.217.29334
2.072.1510010.4511.276.86352
22.0797.710.5281.335.8290
4.328.2699.720.0340.616.6888
3.424.399.120.0360.596.6946
2.993.4299.720.0570.667.06117
2.712.9999.920.1040.87.19215
2.522.7110020.1610.957.21259
2.372.5210020.2411.067.22283
2.252.3710020.321.177.23293
2.152.2510020.4051.267.24343
2.072.1510020.5041.347.22359
22.0710020.5971.386.64438
ReflectionResolution: 2→31.3 Å / Num. obs: 45900 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.04 % / Biso Wilson estimate: 27.7 Å2 / Rmerge(I) obs: 0.061 / Χ2: 0.98 / Net I/σ(I): 10.7 / Scaling rejects: 2441
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2-2.076.640.59723047345241.38100
2.07-2.157.220.5042.63303345261.34100
2.15-2.257.240.4053.33318245341.26100
2.25-2.377.230.324.13322145561.17100
2.37-2.527.220.2415.23308345431.06100
2.52-2.717.210.1617.43316645610.95100
2.71-2.997.190.10410.73318745850.899.9
2.99-3.427.060.05717.63257745950.6699.7
3.42-4.36.690.03626.23097146240.5999.1
4.3-28.266.680.03428.83251948520.6199.7

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Phasing

PhasingMethod: SAD
Phasing set
ID
1
2
Phasing MADD res high: 2.24 Å / FOM : 0.374 / Reflection: 20741
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double primeF prime
2 wavelength110.9803014.29-4.33
2 wavelength120.95
Phasing MAD set shell
IDResolution (Å)Power (kW)Reflection
PEAK_ANO7.35-30.852.432075
PEAK_ANO4.57-7.352.342074
PEAK_ANO3.85-4.572.22074
PEAK_ANO3.45-3.852.092074
PEAK_ANO3.16-3.451.982074
PEAK_ANO2.95-3.161.832074
PEAK_ANO2.76-2.951.742074
PEAK_ANO2.6-2.761.522074
PEAK_ANO2.44-2.61.152074
PEAK_ANO2.24-2.440.82074
Phasing MAD shell
Resolution (Å)FOM Reflection
2.24-2.440.1792074
2.44-2.60.2372074
2.6-2.760.32074
2.76-2.950.3432074
2.95-3.160.3712074
3.16-3.450.422074
3.45-3.850.4352074
3.85-4.570.462074
4.57-7.340.4872074
7.34-30.850.5112074
Phasing dmDelta phi final: 6.41 / Delta phi initial: 57.21 / FOM : 0.938 / Mask type: RMS / Method: FLIP / Reflection: 86847
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
6.99-401.2120.9472013
5.56-6.993.6240.9722041
4.86-5.563.7660.9742011
4.41-4.863.7340.9762013
4.1-4.414.4080.9732011
3.85-4.15.8030.9672039
3.66-3.856.5470.9772013
3.5-3.665.4710.942009
3.37-3.56.7740.9632054
3.25-3.378.1050.9421991
3.15-3.257.8650.932031
3.06-3.158.7660.932019
2.98-3.067.4940.9332024
2.91-2.988.670.8862002
2.84-2.917.4750.892050
2.78-2.848.4740.8922020
2.72-2.788.2410.9051997
2.67-2.727.8080.8962026
2.63-2.678.1540.8732035
2.58-2.637.9140.8722006
2.54-2.588.6560.8632042
2.5-2.548.5740.8742002
2.46-2.57.9820.8792020
2.43-2.468.5470.8512024
2.4-2.438.3510.8682003
2.37-2.47.990.8742057
2.34-2.377.4370.8431964
2.31-2.347.0770.9192037
2.28-2.316.0860.9282011
2.25-2.286.9820.8682041
2.23-2.255.3630.9892010
2.21-2.235.3770.9592038
2.18-2.214.8860.9981981
2.16-2.184.7910.9982039
2.14-2.164.880.9971990
2.12-2.144.7270.9982042
2.1-2.124.6660.9972026
2.08-2.14.7870.9981990
2.07-2.085.0910.9972017
2.05-2.075.1560.9982004
2.03-2.055.4270.9972044
2.02-2.035.7830.9972041
2-2.026.5160.9972019

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Processing

Software
NameVersionClassificationNB
d*TREK9.5Ldata scaling
SnBphasing
CNSrefinement
PDB_EXTRACT2data extraction
d*TREKdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2→31.3 Å / Isotropic thermal model: overall / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Only the peak data set at 0.9803 angstroms was used for SAD phasing. Refinement was done against the remote data at 0.95 angstroms.
RfactorNum. reflection% reflectionSelection details
Rfree0.248 2070 4.5 %Random
Rwork0.209 ---
all0.242 ---
obs0.242 41179 89.9 %-
Solvent computationBsol: 61.927 Å2
Displacement parametersBiso mean: 47.626 Å2
Baniso -1Baniso -2Baniso -3
1-2.533 Å20 Å20 Å2
2--7.813 Å20 Å2
3----10.346 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2→31.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3537 0 0 312 3849
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.4731.5
X-RAY DIFFRACTIONc_scbond_it2.3822
X-RAY DIFFRACTIONc_mcangle_it2.372
X-RAY DIFFRACTIONc_scangle_it3.4272.5
X-RAY DIFFRACTIONc_bond_d0.010081
X-RAY DIFFRACTIONc_angle_deg1.36265
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRfactor Rfree errorNum. reflection obs% reflection obs (%)
2-2.130.3352170.3140.023449759.8
2.13-2.290.3142990.290.018644685.4
2.29-2.520.2953750.2580.015745198.6
2.52-2.880.2683990.2290.013754099.4
2.88-3.630.2373970.2070.012759299.2
3.63-31.260.2283820.1850.012764196.4
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param

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