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- PDB-6thk: Structural mechanism of pyocin S5 import into Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 6thk
TitleStructural mechanism of pyocin S5 import into Pseudomonas aeruginosa
ComponentsPyocin S5
KeywordsANTIMICROBIAL PROTEIN / Bacteriocin / Pyocin / Antibiotic / Ionophore
Function / homology
Function and homology information


pore-forming activity / defense response to Gram-negative bacterium / killing of cells of another organism / metal ion binding / membrane
Similarity search - Function
Channel forming colicin, C-terminal cytotoxic / Channel forming colicin, C-terminal domain superfamily / Colicin pore forming domain / Channel forming colicins signature.
Similarity search - Domain/homology
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsBehrens, H.M. / Kleanthous, C. / Lowe, E.D.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome TrustInfection, Immunology and Translational Medicine studentship United Kingdom
Wellcome Trust201505/Z/16/Z United Kingdom
Citation
Journal: Mbio / Year: 2020
Title: Pyocin S5 Import into Pseudomonas aeruginosa Reveals a Generic Mode of Bacteriocin Transport.
Authors: Behrens, H.M. / Lowe, E.D. / Gault, J. / Housden, N.G. / Kaminska, R. / Weber, T.M. / Thompson, C.M.A. / Mislin, G.L.A. / Schalk, I.J. / Walker, D. / Robinson, C.V. / Kleanthous, C.
#1: Journal: Biorxiv / Year: 2019
Title: Pyocin S5 import into Pseudomonas aeruginosa reveals a generic mode of bacteriocin transport
Authors: Behrens, H.M. / Lowe, E.D. / Gault, J. / Housden, N.G. / Kaminska, R. / Weber, T.M. / Thompson, C. / Mislin, G.L.A. / Schalk, I.J. / Walker, D. / Robinson, C.V. / Kleanthous, C.
History
DepositionNov 20, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2020Group: Database references / Category: citation / citation_author
Revision 1.2May 15, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI ..._citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pyocin S5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,83810
Polymers57,2231
Non-polymers6159
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area870 Å2
ΔGint-184 kcal/mol
Surface area26890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.240, 53.870, 104.800
Angle α, β, γ (deg.)90.000, 95.150, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Pyocin S5


Mass: 57223.105 Da / Num. of mol.: 1 / Mutation: E215Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: pyoS5, PA0985 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9I4Y4
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.47 Å3/Da / Density % sol: 50.17 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 10% w/v PEG 3000, 0.1 M sodium acetate, 0.1 M zinc acetate, pH 4.5 protein buffer: 25 mL Tris-HCl pH 7.5, 150 mM NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9679 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: May 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9679 Å / Relative weight: 1
ReflectionResolution: 2.2→53.7 Å / Num. obs: 28285 / % possible obs: 98.8 % / Redundancy: 4.4 % / Biso Wilson estimate: 41.76 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.113 / Rrim(I) all: 0.179 / Χ2: 1.01 / Net I/σ(I): 4.9
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 4.6 % / Rmerge(I) obs: 1.946 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 2467 / CC1/2: 0.728 / Rpim(I) all: 1.594 / Rrim(I) all: 2.52 / Χ2: 1.11 / % possible all: 99.7

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→52.19 Å / Cor.coef. Fo:Fc: 0.897 / Cor.coef. Fo:Fc free: 0.856 / SU R Cruickshank DPI: 0.265 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.256 / SU Rfree Blow DPI: 0.216 / SU Rfree Cruickshank DPI: 0.221
RfactorNum. reflection% reflectionSelection details
Rfree0.275 1301 4.62 %RANDOM
Rwork0.225 ---
obs0.227 28161 98.3 %-
Displacement parametersBiso max: 134.41 Å2 / Biso mean: 63.91 Å2 / Biso min: 30 Å2
Baniso -1Baniso -2Baniso -3
1-22.1836 Å20 Å214.0936 Å2
2--2.9421 Å20 Å2
3----25.1257 Å2
Refinement stepCycle: final / Resolution: 2.2→52.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3633 0 14 84 3731
Biso mean--66.87 60.53 -
Num. residues----466
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1335SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes104HARMONIC2
X-RAY DIFFRACTIONt_gen_planes534HARMONIC5
X-RAY DIFFRACTIONt_it3712HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion499SEMIHARMONIC5
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_contact4362SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3712HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg5014HARMONIC21.08
X-RAY DIFFRACTIONt_omega_torsion2.51
X-RAY DIFFRACTIONt_other_torsion21
LS refinement shellResolution: 2.2→2.28 Å / Rfactor Rfree error: 0 / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.3093 138 4.62 %
Rwork0.2573 2848 -
all0.26 2986 -
obs--98.74 %

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