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- PDB-4jur: Crystal structure of the effector Tae4 from Salmonella typhimuriu... -

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Basic information

Entry
Database: PDB / ID: 4jur
TitleCrystal structure of the effector Tae4 from Salmonella typhimurium in complex with the immunity Tai4 from Enterobacter cloacae
Components
  • Putative cytoplasmic protein
  • Uncharacterized protein
KeywordsHYDROLASE / toxin-antitoxin
Function / homology
Function and homology information


endopeptidase fold (from Nostoc punctiforme) - #70 / Type VI secretion system (T6SS), amidase immunity protein / T6SS superfamily / Type VI secretion system (T6SS), amidase immunity protein / Four Helix Bundle (Hemerythrin (Met), subunit A) - #1620 / Type VI secretion system (T6SS), amidase effector protein 4 / Type VI secretion system (T6SS), amidase effector protein 4 / endopeptidase fold (from Nostoc punctiforme) / Four Helix Bundle (Hemerythrin (Met), subunit A) / Alpha-Beta Complex ...endopeptidase fold (from Nostoc punctiforme) - #70 / Type VI secretion system (T6SS), amidase immunity protein / T6SS superfamily / Type VI secretion system (T6SS), amidase immunity protein / Four Helix Bundle (Hemerythrin (Met), subunit A) - #1620 / Type VI secretion system (T6SS), amidase effector protein 4 / Type VI secretion system (T6SS), amidase effector protein 4 / endopeptidase fold (from Nostoc punctiforme) / Four Helix Bundle (Hemerythrin (Met), subunit A) / Alpha-Beta Complex / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein / Uncharacterized protein / Cytoplasmic protein
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
Enterobacter cloacae subsp. cloacae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsZhang, H. / Gao, Z.Q. / Dong, Y.H.
CitationJournal: Plos One / Year: 2013
Title: Insights into the cross-immunity mechanism within effector families of bacteria type VI secretion system from the structure of StTae4-EcTai4 complex
Authors: Zhang, H. / Gao, Z.Q. / Wei, Y. / Xu, J.H. / Dong, Y.H.
History
DepositionMar 25, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative cytoplasmic protein
B: Putative cytoplasmic protein
C: Putative cytoplasmic protein
D: Putative cytoplasmic protein
E: Putative cytoplasmic protein
F: Putative cytoplasmic protein
G: Putative cytoplasmic protein
H: Putative cytoplasmic protein
I: Uncharacterized protein
J: Uncharacterized protein
K: Uncharacterized protein
L: Uncharacterized protein
M: Uncharacterized protein
N: Uncharacterized protein
O: Uncharacterized protein
P: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)250,33816
Polymers250,33816
Non-polymers00
Water3,963220
1
A: Putative cytoplasmic protein
H: Putative cytoplasmic protein
I: Uncharacterized protein
P: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)62,5854
Polymers62,5854
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative cytoplasmic protein
F: Putative cytoplasmic protein
J: Uncharacterized protein
N: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)62,5854
Polymers62,5854
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Putative cytoplasmic protein
D: Putative cytoplasmic protein
K: Uncharacterized protein
L: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)62,5854
Polymers62,5854
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
E: Putative cytoplasmic protein
G: Putative cytoplasmic protein
M: Uncharacterized protein
O: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)62,5854
Polymers62,5854
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.951, 89.125, 271.948
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Putative cytoplasmic protein


Mass: 19591.201 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: STM0277 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q93IS4, amidase
#2: Protein
Uncharacterized protein


Mass: 11701.106 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter cloacae subsp. cloacae (bacteria)
Strain: ATCC 13047 / DSM 30054 / NBRC 13535 / NCDC 279-56 / Gene: ECL_01543 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D5C6F7, UniProt: A0A0H3CIX8*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / Source method: isolated from a natural source / Formula: H2O
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: 2.15 Å3/Da / Density % sol: 42.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20%(w/v) PEG3350, 0.2M Magnesium formate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 24, 2013
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 75000 / Num. obs: 75000 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 41
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.561 / Mean I/σ(I) obs: 5.26 / Num. unique all: 3723 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
SOLVEphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.5→46.194 Å / SU ML: 0.39 / σ(F): 1.33 / Phase error: 29.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2613 3765 5.04 %random
Rwork0.207 ---
all0.2098 75000 --
obs0.207 74765 99.3 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.246 Å2 / ksol: 0.314 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.2624 Å20 Å2-0 Å2
2--1.9535 Å20 Å2
3----3.216 Å2
Refinement stepCycle: LAST / Resolution: 2.5→46.194 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15755 0 0 220 15975
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116147
X-RAY DIFFRACTIONf_angle_d1.24621939
X-RAY DIFFRACTIONf_dihedral_angle_d15.3585763
X-RAY DIFFRACTIONf_chiral_restr0.0862416
X-RAY DIFFRACTIONf_plane_restr0.0052864
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.53690.33581180.27262356X-RAY DIFFRACTION89
2.5369-2.57030.40891320.29632581X-RAY DIFFRACTION100
2.5703-2.60550.43191340.29882615X-RAY DIFFRACTION100
2.6055-2.64270.39061210.29422608X-RAY DIFFRACTION100
2.6427-2.68220.36011460.29462630X-RAY DIFFRACTION100
2.6822-2.72410.37041180.26932620X-RAY DIFFRACTION100
2.7241-2.76870.35551450.27832600X-RAY DIFFRACTION100
2.7687-2.81650.3561380.26792570X-RAY DIFFRACTION100
2.8165-2.86770.31781640.25112640X-RAY DIFFRACTION100
2.8677-2.92280.40691400.2562586X-RAY DIFFRACTION100
2.9228-2.98250.3211230.25472667X-RAY DIFFRACTION100
2.9825-3.04730.29621290.25182586X-RAY DIFFRACTION100
3.0473-3.11820.35571390.25762621X-RAY DIFFRACTION100
3.1182-3.19610.3051310.26872639X-RAY DIFFRACTION100
3.1961-3.28250.32591450.24162637X-RAY DIFFRACTION100
3.2825-3.37910.29221610.23342582X-RAY DIFFRACTION100
3.3791-3.48810.29151310.2212659X-RAY DIFFRACTION100
3.4881-3.61270.24341190.1972637X-RAY DIFFRACTION100
3.6127-3.75730.21931330.19442651X-RAY DIFFRACTION100
3.7573-3.92820.22751440.18622650X-RAY DIFFRACTION100
3.9282-4.13520.24581390.16812637X-RAY DIFFRACTION100
4.1352-4.39410.19461550.16082655X-RAY DIFFRACTION100
4.3941-4.73310.2031510.15372652X-RAY DIFFRACTION100
4.7331-5.20880.23251440.16792705X-RAY DIFFRACTION100
5.2088-5.96120.24621290.20222722X-RAY DIFFRACTION100
5.9612-7.50520.19471650.17752709X-RAY DIFFRACTION100
7.5052-46.2020.22451710.18052785X-RAY DIFFRACTION98

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