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- PDB-5odw: Structure of the FpvAI-pyocin S2 complex -

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Basic information

Entry
Database: PDB / ID: 5odw
TitleStructure of the FpvAI-pyocin S2 complex
Components
  • Ferripyoverdine receptor
  • Pyocin-S2
KeywordsPROTEIN TRANSPORT / Antimicrobial protein / membrane protein complex
Function / homology
Function and homology information


pyoverdine biosynthetic process / siderophore uptake transmembrane transporter activity / cytolysis / cell outer membrane / signaling receptor activity / endonuclease activity / killing of cells of another organism / Hydrolases; Acting on ester bonds / defense response to bacterium / signaling receptor binding ...pyoverdine biosynthetic process / siderophore uptake transmembrane transporter activity / cytolysis / cell outer membrane / signaling receptor activity / endonuclease activity / killing of cells of another organism / Hydrolases; Acting on ester bonds / defense response to bacterium / signaling receptor binding / membrane / metal ion binding
Similarity search - Function
Pyocin S killer protein / S-type Pyocin / Secretin and TonB N terminus short domain / Secretin/TonB, short N-terminal domain / Secretin and TonB N terminus short domain / Colicin/Pyocin-S2, DNase domain / Colicin/pyocin, DNase domain superfamily / TonB-dependent receptor, beta-barrel domain / TonB-dependent receptor, plug domain / Pyosin/cloacin translocation domain ...Pyocin S killer protein / S-type Pyocin / Secretin and TonB N terminus short domain / Secretin/TonB, short N-terminal domain / Secretin and TonB N terminus short domain / Colicin/Pyocin-S2, DNase domain / Colicin/pyocin, DNase domain superfamily / TonB-dependent receptor, beta-barrel domain / TonB-dependent receptor, plug domain / Pyosin/cloacin translocation domain / Pyosin/cloacin translocation domain superfamily / Maltoporin; Chain A / HNH nucleases / TonB-dependent siderophore receptor / Ferric Hydroxamate Uptake Protein; Chain A, domain 1 / TonB-dependent receptor, conserved site / TonB-dependent receptor (TBDR) proteins signature 2. / TonB-dependent receptor (TBDR) proteins profile. / Vitamin B12 transporter BtuB-like / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor-like, beta-barrel / TonB-dependent receptor, plug domain superfamily / TonB-dependent receptor, plug domain / TonB-dependent receptor-like, beta-barrel domain superfamily / TonB-dependent Receptor Plug Domain / His-Me finger superfamily / HNH nuclease / Beta Complex / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Ferripyoverdine receptor / Pyocin-S2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsWhite, P. / Joshi, A. / Kleanthous, C.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust201505/Z/16/Z United Kingdom
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Exploitation of an iron transporter for bacterial protein antibiotic import.
Authors: White, P. / Joshi, A. / Rassam, P. / Housden, N.G. / Kaminska, R. / Goult, J.D. / Redfield, C. / McCaughey, L.C. / Walker, D. / Mohammed, S. / Kleanthous, C.
History
DepositionJul 6, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 8, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Ferripyoverdine receptor
B: Ferripyoverdine receptor
C: Pyocin-S2
D: Pyocin-S2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,05314
Polymers231,0924
Non-polymers96110
Water0
1
A: Ferripyoverdine receptor
C: Pyocin-S2
hetero molecules


  • defined by author&software
  • Evidence: cross-linking, Cross-links observed at interfacial residues, gel filtration, Proteins co-elute in single peak, isothermal titration calorimetry, High affinity binding constant, mass ...Evidence: cross-linking, Cross-links observed at interfacial residues, gel filtration, Proteins co-elute in single peak, isothermal titration calorimetry, High affinity binding constant, mass spectrometry, Observed mass by native ESI-MS agrees with predicted mass
  • 116 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)116,0267
Polymers115,5462
Non-polymers4805
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-92 kcal/mol
Surface area40280 Å2
MethodPISA
2
B: Ferripyoverdine receptor
D: Pyocin-S2
hetero molecules


  • defined by author&software
  • Evidence: cross-linking, Cross-links observed at interfacial residues, gel filtration, Proteins co-elute in single peak, isothermal titration calorimetry, High affinity binding constant, mass ...Evidence: cross-linking, Cross-links observed at interfacial residues, gel filtration, Proteins co-elute in single peak, isothermal titration calorimetry, High affinity binding constant, mass spectrometry, Observed mass by native ESI-MS agrees with predicted mass
  • 116 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)116,0267
Polymers115,5462
Non-polymers4805
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-92 kcal/mol
Surface area39410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.524, 209.390, 215.845
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Ferripyoverdine receptor


Mass: 91260.789 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Cell: Bacterial / Gene: fpvA, PA2398 / Production host: Escherichia coli (E. coli) / Variant (production host): TNE012 / References: UniProt: P48632
#2: Protein Pyocin-S2 / Killer protein


Mass: 24285.293 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Gene: pys2, PA1150 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q06584, Hydrolases; Acting on ester bonds
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4

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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: 2.89 Å3/Da / Density % sol: 57.37 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 0.350 M ammonium sulphate, 13.5% (w/v) PEG3350, 0.050 M sodium acetate pH 4.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 4, 2015
RadiationMonochromator: Silicon 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
ReflectionResolution: 2.8→47.97 Å / Num. obs: 63709 / % possible obs: 98.8 % / Redundancy: 5.7 % / Biso Wilson estimate: 60.22 Å2 / CC1/2: 0.965 / Rmerge(I) obs: 0.347 / Rpim(I) all: 0.236 / Net I/σ(I): 5.5
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 6 % / Rmerge(I) obs: 1.701 / Mean I/σ(I) obs: 1.3 / Num. unique all: 4490 / CC1/2: 0.412 / Rpim(I) all: 1.059 / % possible all: 99.5

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDS0.52data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2W16

2w16


Resolution: 2.8→47.97 Å / Cor.coef. Fo:Fc: 0.867 / Cor.coef. Fo:Fc free: 0.808 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 1.263 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.978 / SU Rfree Blow DPI: 0.346 / SU Rfree Cruickshank DPI: 0.358
RfactorNum. reflection% reflectionSelection details
Rfree0.262 3094 4.86 %RANDOM
Rwork0.212 ---
obs0.214 63709 98.5 %-
Displacement parametersBiso mean: 38.11 Å2
Baniso -1Baniso -2Baniso -3
1-16.6565 Å20 Å20 Å2
2---8.4365 Å20 Å2
3----8.2199 Å2
Refine analyzeLuzzati coordinate error obs: 0.41 Å
Refinement stepCycle: 1 / Resolution: 2.8→47.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15038 0 50 0 15088
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0115427HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.220924HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5281SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes429HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2237HARMONIC5
X-RAY DIFFRACTIONt_it15427HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.98
X-RAY DIFFRACTIONt_other_torsion20.88
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1963SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact16242SEMIHARMONIC4
LS refinement shellResolution: 2.8→2.87 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 231 4.9 %
Rwork0.242 4488 -
all0.245 4719 -
obs--99.41 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7495-0.79140.14214.4498-0.61837.09350.02840.19510.1565-0.4711-0.06320.20860.24680.31210.0348-0.09470.0092-0.0201-0.11370.021-0.0597-29.2105-19.3939-59.608
20.6078-0.21710.09250.4451-0.05120.3531-0.0357-0.11820.02750.08590.02050.0241-0.0235-0.0660.0152-0.074-0.01580.0151-0.0769-0.0247-0.0686-23.883-40.4287-29.2064
31.001-2.4937-0.64631.39740.6230.30770.04230.04320.10290.1064-0.13-0.18430.06590.11360.0876-0.1109-0.07270.071-0.0091-0.01220.0484-15.3232-54.6856-86.3756
40.57950.0384-0.0880.33040.01860.1974-0.03720.0348-0.09870.01220.041-0.03610.0297-0.0357-0.0038-0.06610.0046-0.0051-0.0829-0.0156-0.0336-23.5542-79.0892-61.1248
51.381-0.6089-0.21991.6258-0.48580-0.0275-0.0544-0.00390.2020.00850.05050.11810.04430.0190.201-0.0451-0.02890.06090.07810.0491-29.3634-69.555910.5683
60.06010.9728-1.19411.7213-2.79523.55450.0173-0.0566-0.0624-0.02710.19190.25550.0871-0.2202-0.20920.05740.00860.0264-0.01050.1531-0.1092-37.7823-79.123710.8282
75.8911-0.62051.494800.04010.5838-0.0210.183-0.04130.2010.01810.0440.1878-0.02990.0029-0.0829-0.0086-0.06980.11090.05450.1983-20.9107-114.358-25.8692
80.1662-0.64650.95772.8187-3.00282.5823-0.0043-0.0215-0.1010.1601-0.0603-0.01010.02590.04810.06450.02640.0123-0.026-0.10990.1096-0.0261-13.1333-112.897-15.4848
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|45 - 124}
2X-RAY DIFFRACTION2{A|125 - 815}
3X-RAY DIFFRACTION3{B|54 - 116}
4X-RAY DIFFRACTION4{B|125 - 815}
5X-RAY DIFFRACTION5{C|11 - 34}
6X-RAY DIFFRACTION6{C|35 - 99}
7X-RAY DIFFRACTION7{D|11 - 34}
8X-RAY DIFFRACTION8{D|35 - 206}

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