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- PDB-7jtu: Cytidine deaminase T6S toxin from Pseudomonas syringae -

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Basic information

Entry
Database: PDB / ID: 7jtu
TitleCytidine deaminase T6S toxin from Pseudomonas syringae
Components
  • SsdA
  • SsdAI
KeywordsTOXIN / Immunity / Type VI / T6SS / deaminase
Function / homology
Function and homology information


Immunity protein Imm5 / Immunity protein Imm5 / : / Single-strand DNA deaminase toxin A, C-terminal / Class I prePAAR effector Rhs1 motif / DYW family of nucleic acid deaminases / PAAR motif / PAAR motif
Similarity search - Domain/homology
Rhs protein / Immunity protein Imm5 domain-containing protein
Similarity search - Component
Biological speciesPseudomonas syringae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å
AuthorsBosch, D.E. / Hsu, F. / de Moraes, M.H. / Mougous, J.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)NIH R01 AI080609 United States
CitationJournal: Elife / Year: 2021
Title: An interbacterial DNA deaminase toxin directly mutagenizes surviving target populations.
Authors: de Moraes, M.H. / Hsu, F. / Huang, D. / Bosch, D.E. / Zeng, J. / Radey, M.C. / Simon, N. / Ledvina, H.E. / Frick, J.P. / Wiggins, P.A. / Peterson, S.B. / Mougous, J.D.
History
DepositionAug 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title ..._citation.journal_volume / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SsdA
B: SsdAI


Theoretical massNumber of molelcules
Total (without water)40,6182
Polymers40,6182
Non-polymers00
Water543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-5 kcal/mol
Surface area15080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.069, 93.069, 383.492
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein SsdA


Mass: 18559.082 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0Q0DAS4
#2: Protein SsdAI


Mass: 22058.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3M2XVH3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 5.15 Å3/Da / Density % sol: 76.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Hanging drop diffusion. SsdA/SsdAI complex at 10 mg/mL was mixed 1:1 with crystallization solutions containing 20% PEG 3350, 0.1 M Bis-Tris:HCl pH 7.5 and 200 mM MgCl2. Cryopreservation was ...Details: Hanging drop diffusion. SsdA/SsdAI complex at 10 mg/mL was mixed 1:1 with crystallization solutions containing 20% PEG 3350, 0.1 M Bis-Tris:HCl pH 7.5 and 200 mM MgCl2. Cryopreservation was in crystallization solution with 20% glycerol.
Temp details: Room temperature

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3→35 Å / Num. obs: 17597 / % possible obs: 100 % / Redundancy: 28.6 % / Biso Wilson estimate: 79.6 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 22.9
Reflection shellResolution: 3→3.03 Å / Redundancy: 29.6 % / Num. unique obs: 434 / Rpim(I) all: 0.279 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3→33.39 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 24.99 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2348 1708 9.9 %
Rwork0.2021 15540 -
obs0.2054 17248 98.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 136.64 Å2 / Biso mean: 79.8133 Å2 / Biso min: 42.85 Å2
Refinement stepCycle: final / Resolution: 3→33.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2717 0 0 3 2720
Biso mean---65.45 -
Num. residues----344
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3-3.080.40541330.34271193132694
3.08-3.180.29731330.29151242137597
3.18-3.30.33381350.2841265140097
3.3-3.430.32981370.25471269140698
3.43-3.580.28791420.24371269141198
3.58-3.770.23791370.21121285142298
3.77-4.010.22071400.19461279141998
4.01-4.320.19721450.17681298144399
4.32-4.750.19961460.17311318146499
4.75-5.440.22181480.175413251473100
5.44-6.840.23181500.200113441494100
6.84-33.390.20771620.178514531615100

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