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- PDB-5ces: C-terminal domain of the R-type pyocin baseplate protein PA0618 -

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Basic information

Entry
Database: PDB / ID: 5ces
TitleC-terminal domain of the R-type pyocin baseplate protein PA0618
ComponentsPA0618
KeywordsSTRUCTURAL PROTEIN / gpJ / gp6
Function / homologyBaseplate assembly protein J, predicted / Baseplate protein J-like / Baseplate J-like protein / Probable bacteriophage protein
Function and homology information
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.102 Å
AuthorsPlattner, M. / Buth, S.A. / Shneider, M.M. / Leiman, P.G.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation310030_144243 Switzerland
CitationJournal: Nature / Year: 2020
Title: Action of a minimal contractile bactericidal nanomachine.
Authors: Peng Ge / Dean Scholl / Nikolai S Prokhorov / Jaycob Avaylon / Mikhail M Shneider / Christopher Browning / Sergey A Buth / Michel Plattner / Urmi Chakraborty / Ke Ding / Petr G Leiman / Jeff ...Authors: Peng Ge / Dean Scholl / Nikolai S Prokhorov / Jaycob Avaylon / Mikhail M Shneider / Christopher Browning / Sergey A Buth / Michel Plattner / Urmi Chakraborty / Ke Ding / Petr G Leiman / Jeff F Miller / Z Hong Zhou /
Abstract: R-type bacteriocins are minimal contractile nanomachines that hold promise as precision antibiotics. Each bactericidal complex uses a collar to bridge a hollow tube with a contractile sheath loaded ...R-type bacteriocins are minimal contractile nanomachines that hold promise as precision antibiotics. Each bactericidal complex uses a collar to bridge a hollow tube with a contractile sheath loaded in a metastable state by a baseplate scaffold. Fine-tuning of such nucleic acid-free protein machines for precision medicine calls for an atomic description of the entire complex and contraction mechanism, which is not available from baseplate structures of the (DNA-containing) T4 bacteriophage. Here we report the atomic model of the complete R2 pyocin in its pre-contraction and post-contraction states, each containing 384 subunits of 11 unique atomic models of 10 gene products. Comparison of these structures suggests the following sequence of events during pyocin contraction: tail fibres trigger lateral dissociation of baseplate triplexes; the dissociation then initiates a cascade of events leading to sheath contraction; and this contraction converts chemical energy into mechanical force to drive the iron-tipped tube across the bacterial cell surface, killing the bacterium.
History
DepositionJul 7, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1May 16, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.2May 23, 2018Group: Data collection / Database references / Structure summary
Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.3Apr 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.4May 13, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.5May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PA0618
B: PA0618


Theoretical massNumber of molelcules
Total (without water)22,6032
Polymers22,6032
Non-polymers00
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1060 Å2
ΔGint-6 kcal/mol
Surface area10010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.611, 72.611, 46.519
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein PA0618


Mass: 11301.653 Da / Num. of mol.: 2
Fragment: Proteolytically stable C-terminal fragment, UNP residues 202-295
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: PA0618 / Production host: Escherichia coli (E. coli) / References: UniProt: G3XCX5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.66 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: PEG 5000 MME, ammonium acetate, MES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.91963 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91963 Å / Relative weight: 1
ReflectionResolution: 2.102→39.17 Å / Num. obs: 27538 / % possible obs: 99.6 % / Redundancy: 5.378 % / Net I/σ(I): 30.41

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.102→39.17 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.236 499 3.5 %
Rwork0.1904 --
obs0.192 14247 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.102→39.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1392 0 0 58 1450
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031426
X-RAY DIFFRACTIONf_angle_d0.7051937
X-RAY DIFFRACTIONf_dihedral_angle_d13.979527
X-RAY DIFFRACTIONf_chiral_restr0.027221
X-RAY DIFFRACTIONf_plane_restr0.003257
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1023-2.31380.30011230.24123390X-RAY DIFFRACTION99
2.3138-2.64850.25031230.21683396X-RAY DIFFRACTION100
2.6485-3.33660.2841250.24323458X-RAY DIFFRACTION100
3.3366-39.17670.21141280.1653504X-RAY DIFFRACTION100
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)
15.56214.21652.13346.51013.84393.17680.17530.3277-0.42910.64380.1014-0.61271.63161.0778-0.27050.58950.11120.01190.3568-0.00720.580635.949662.14144.1646
24.1835-1.446-0.19482.0319-2.25488.7393-0.30390.16310.2666-0.0543-0.05150.04480.47360.20830.3660.6611-0.0482-0.0340.51320.03190.709828.748670.9645-3.5306
36.75612.31433.75643.20623.75038.6653-0.1199-0.23270.02860.4563-0.09170.11730.698-0.33880.18950.4997-0.01650.07190.34120.01960.472629.939763.34444.0596
48.17595.56596.21995.13562.73888.09410.939-0.7916-0.0060.6067-0.2489-0.07380.59030.1087-0.59420.7728-0.14230.15840.8268-0.1240.877510.009552.30113.1083
59.22714.9359-3.13529.2749-6.44885.4611-0.63810.36623.76621.84861.11620.8736-2.38031.0031-0.29891.865-0.52840.28311.4489-0.45231.492916.217971.538218.5936
64.97581.56843.19687.75123.68179.68740.4874-0.79761.51390.2192-0.58211.6726-0.578-1.41030.43440.7863-0.06310.20560.902-0.24021.36817.203864.12072.6289
77.2652.1949-0.29497.53553.08635.85790.3446-0.57850.32910.498-0.38560.39610.3444-0.16220.08290.5747-0.17550.13830.6576-0.05060.658713.804556.78882.044
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 202 through 215 )
2X-RAY DIFFRACTION2chain 'A' and (resid 216 through 243 )
3X-RAY DIFFRACTION3chain 'A' and (resid 244 through 292 )
4X-RAY DIFFRACTION4chain 'B' and (resid 202 through 215 )
5X-RAY DIFFRACTION5chain 'B' and (resid 216 through 221 )
6X-RAY DIFFRACTION6chain 'B' and (resid 222 through 243 )
7X-RAY DIFFRACTION7chain 'B' and (resid 244 through 292 )

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