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- PDB-7rt7: Crystal structure of the RhsP2 C-terminal toxin domain in complex... -

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Basic information

Entry
Database: PDB / ID: 7rt7
TitleCrystal structure of the RhsP2 C-terminal toxin domain in complex with its immunity protein, RhsI2
Components
  • RhsI2
  • RhsP2
KeywordsTOXIN/ANTITOXIN / Type Six Secretion System / Effector / Immunity / ADP-ribosyl transferase / RNA / Translation / Complex / TOXIN-ANTITOXIN complex
Function / homology
Function and homology information


Domain of unknown function DUF6531 / RHS protein / Domain of unknown function (DUF6531) / RHS protein / RHS repeat / RHS Repeat / YD repeat / Rhs repeat-associated core / :
Similarity search - Domain/homology
Putative Rhs family protein / Uncharacterized protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.49 Å
AuthorsBullen, N.P. / Prehna, G. / Whitney, J.C.
Funding support Canada, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT-175011 Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2018-04968 Canada
CitationJournal: Mol.Cell / Year: 2022
Title: An ADP-ribosyltransferase toxin kills bacterial cells by modifying structured non-coding RNAs.
Authors: Bullen, N.P. / Sychantha, D. / Thang, S.S. / Culviner, P.H. / Rudzite, M. / Ahmad, S. / Shah, V.S. / Filloux, A. / Prehna, G. / Whitney, J.C.
History
DepositionAug 12, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2023Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RhsP2
D: RhsI2
B: RhsP2
C: RhsI2
E: RhsP2
F: RhsI2
G: RhsP2
H: RhsI2
I: RhsP2
J: RhsI2
K: RhsP2
L: RhsI2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,93515
Polymers201,56912
Non-polymers3663
Water3,963220
1
A: RhsP2
D: RhsI2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8394
Polymers33,5952
Non-polymers2442
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RhsP2
C: RhsI2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7173
Polymers33,5952
Non-polymers1221
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: RhsP2
F: RhsI2


Theoretical massNumber of molelcules
Total (without water)33,5952
Polymers33,5952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: RhsP2
H: RhsI2


Theoretical massNumber of molelcules
Total (without water)33,5952
Polymers33,5952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
I: RhsP2
J: RhsI2


Theoretical massNumber of molelcules
Total (without water)33,5952
Polymers33,5952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
K: RhsP2
L: RhsI2


Theoretical massNumber of molelcules
Total (without water)33,5952
Polymers33,5952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.456, 112.456, 324.331
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"

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Components

#1: Protein
RhsP2


Mass: 17019.033 Da / Num. of mol.: 6 / Fragment: C-terminal toxin domain (UNP residues 1473-1614)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain UCBPP-PA14) (bacteria)
Strain: UCBPP-PA14 / Gene: PA14_43100 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H2Z8A2
#2: Protein
RhsI2


Mass: 16575.777 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain UCBPP-PA14) (bacteria)
Strain: UCBPP-PA14
Gene: DZ962_29645, IPC1164_23695, IPC737_11070, PA52Ts2_2703
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A367GXM0
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 3.07 Å3/Da / Density % sol: 59.94 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 9.1 / Details: 1.05 M sodium citrate, 0.1 M CHES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.49→97.39 Å / Num. obs: 83716 / % possible obs: 99.85 % / Redundancy: 9.3 % / CC1/2: 0.994 / Net I/σ(I): 8.5
Reflection shellResolution: 2.5→2.55 Å / Num. unique obs: 4486 / CC1/2: 0.574

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.49→97.39 Å / Cross valid method: FREE R-VALUE / σ(F): 377.4 / Phase error: 22.7395
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.232 4262 5.09 %
Rwork0.1952 79454 -
obs0.201 83716 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.14 Å2
Refinement stepCycle: LAST / Resolution: 2.49→97.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13575 0 24 220 13819
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003113853
X-RAY DIFFRACTIONf_angle_d0.661618734
X-RAY DIFFRACTIONf_chiral_restr0.04312091
X-RAY DIFFRACTIONf_plane_restr0.00852419
X-RAY DIFFRACTIONf_dihedral_angle_d5.57041831
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.49-2.540.27371940.24613796X-RAY DIFFRACTION92.25
2.54-2.580.30182290.24293894X-RAY DIFFRACTION94.42
2.58-2.630.2982030.23683948X-RAY DIFFRACTION95.11
2.63-2.690.30232330.24263895X-RAY DIFFRACTION94.33
2.69-2.750.30142440.23453915X-RAY DIFFRACTION94.13
2.75-2.810.26182080.23123935X-RAY DIFFRACTION94.98
2.81-2.880.29092070.22523945X-RAY DIFFRACTION95.01
2.88-2.960.29482050.22563951X-RAY DIFFRACTION95.07
2.96-3.040.23632150.22153937X-RAY DIFFRACTION94.82
3.04-3.140.27012030.21843937X-RAY DIFFRACTION95.1
3.14-3.260.27922120.21363925X-RAY DIFFRACTION94.88
3.26-3.390.22822080.20963991X-RAY DIFFRACTION95.05
3.39-3.540.22932040.20043965X-RAY DIFFRACTION95.11
3.54-3.730.22062120.18763979X-RAY DIFFRACTION94.94
3.73-3.960.22192120.18293969X-RAY DIFFRACTION94.93
3.96-4.260.22412070.16384008X-RAY DIFFRACTION95.09
4.27-4.690.16922180.154022X-RAY DIFFRACTION94.86
4.69-5.370.18372110.16364045X-RAY DIFFRACTION95.04
5.37-6.770.25062130.19944102X-RAY DIFFRACTION95.06
6.77-97.390.22432230.22734296X-RAY DIFFRACTION95.07

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