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- PDB-7dym: Pseudomonas aeruginosa TseT-TsiT complex -

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Basic information

Entry
Database: PDB / ID: 7dym
TitlePseudomonas aeruginosa TseT-TsiT complex
Components
  • Imm52 domain-containing protein
  • Tox-REase-5 domain-containing protein
KeywordsTOXIN / T6SS / immunity / effector / nuclease
Function / homologyTox-REase-5 domain / Restriction endonuclease fold toxin 5 / Imm52 family, TsiT-like / Immunity protein 52 / Immunity protein 52 / Immunity protein 52 domain-containing protein / Tox-REase-5 domain-containing protein
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.1 Å
AuthorsShe, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Basic Research Program of China (973 Program)2017YFA0504900 China
CitationJournal: Int.J.Biol.Macromol. / Year: 2021
Title: Structure and SAXS studies unveiled a novel inhibition mechanism of the Pseudomonas aeruginosa T6SS TseT-TsiT complex.
Authors: Wen, H. / Liu, G. / Geng, Z. / Zhang, H. / Li, Y. / She, Z. / Dong, Y.
History
DepositionJan 22, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tox-REase-5 domain-containing protein
B: Imm52 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)55,0382
Polymers55,0382
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-10 kcal/mol
Surface area20380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.500, 77.500, 185.900
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Tox-REase-5 domain-containing protein / TseT protein


Mass: 27708.621 Da / Num. of mol.: 1
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)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: PA3907 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9HXA6
#2: Protein Imm52 domain-containing protein / TsiT protein


Mass: 27328.992 Da / Num. of mol.: 1
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)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: PA3908 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9HXA5
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: 2.82 Å3/Da / Density % sol: 56.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.18 m Trimethylamine N-oxide, 0.1M Tris pH 8.5, 11% PEG2000MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.1→45.53 Å / Num. obs: 11293 / % possible obs: 98.78 % / Redundancy: 10 % / CC1/2: 0.99 / Rmerge(I) obs: 0.063 / Net I/σ(I): 23.34
Reflection shellResolution: 3.1→3.18 Å / Rmerge(I) obs: 0.48 / Num. unique obs: 777 / CC1/2: 0.96

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 3.1→25.37 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.42 / Phase error: 28.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2372 545 4.83 %
Rwork0.2064 10748 -
obs0.2079 11293 98.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 220.63 Å2 / Biso mean: 111.2169 Å2 / Biso min: 56.97 Å2
Refinement stepCycle: final / Resolution: 3.1→25.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3342 0 0 0 3342
Num. residues----409
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1-3.410.34131610.25642650281199
3.41-3.90.32631070.28782658276597
3.9-4.910.24621270.194827212848100
4.91-25.370.19271500.17732719286999

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