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- PDB-4hff: Crystal structure of the type VI effector-immunity complex Tae4-T... -

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Basic information

Entry
Database: PDB / ID: 4hff
TitleCrystal structure of the type VI effector-immunity complex Tae4-Tai4 from Salmonella Typhimurium
Components
  • Putative cytoplasmic protein
  • Putative periplasmic protein
KeywordsHYDROLASE / amidase
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
Periplasmic protein / Cytoplasmic protein
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.398 Å
AuthorsZhang, H. / Gao, Z.Q. / Dong, Y.H.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structure of the type VI effector-immunity complex (Tae4-Tai4) provides novel insights into the inhibition mechanism of the effector by its immunity protein
Authors: Zhang, H. / Zhang, H. / Gao, Z.Q. / Wang, W.J. / Liu, G.F. / Xu, J.H. / Su, X.D. / Dong, Y.H.
History
DepositionOct 5, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Database references
Revision 1.2Oct 9, 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 periplasmic protein


Theoretical massNumber of molelcules
Total (without water)31,7512
Polymers31,7512
Non-polymers00
Water2,054114
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Putative cytoplasmic protein
B: Putative periplasmic protein

A: Putative cytoplasmic protein
B: Putative periplasmic protein


Theoretical massNumber of molelcules
Total (without water)63,5024
Polymers63,5024
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area6890 Å2
ΔGint-32 kcal/mol
Surface area21340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.903, 63.903, 365.916
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Putative cytoplasmic protein


Mass: 19596.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: STM0277 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q93IS4
#2: Protein Putative periplasmic protein


Mass: 12154.421 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 25-127
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: STM0278 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8ZRL5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 3.4 Å3/Da / Density % sol: 63.78 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2M ammonium acetate, 0.1M sodium citrate tribasic dihydrate (pH 5.6), 30% v/v (+/-)-2-methyl-2,4-pentanedio, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.9793 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 15, 2012
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.398→50 Å / Num. all: 18525 / Num. obs: 18525 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 17.6 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 38.1
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 12.9 % / Rmerge(I) obs: 0.433 / Mean I/σ(I) obs: 4 / Num. unique all: 850 / % possible all: 94.3

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
SOLVEphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.398→38.001 Å / SU ML: 0.37 / σ(F): 1.34 / Phase error: 19.63 / Stereochemistry target values: ML
Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflectionSelection details
Rfree0.2256 950 5.13 %RANDOM
Rwork0.1865 ---
all0.1884 ---
obs0.1884 18525 98.66 %-
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.532 Å2 / ksol: 0.351 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.7307 Å2-0 Å2-0 Å2
2--6.7307 Å20 Å2
3----13.4614 Å2
Refinement stepCycle: LAST / Resolution: 2.398→38.001 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1997 0 0 114 2111
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092052
X-RAY DIFFRACTIONf_angle_d1.0642783
X-RAY DIFFRACTIONf_dihedral_angle_d13.957734
X-RAY DIFFRACTIONf_chiral_restr0.073303
X-RAY DIFFRACTIONf_plane_restr0.005357
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3981-2.46860.40391390.3026235290
2.4686-2.54830.30761390.2392252398
2.5483-2.63930.27291520.2107253198
2.6393-2.7450.22411370.1888253399
2.745-2.86990.22711490.1872259099
2.8699-3.02110.25611450.19272595100
3.0211-3.21030.29681660.19842560100
3.2103-3.4580.29311360.19642574100
3.458-3.80570.22231250.19182593100
3.8057-4.35580.17171320.1612585100
4.3558-5.48520.14361250.14032614100
5.4852-38.00620.19431150.19622624100
Refinement TLS params.Method: refined / Origin x: 48.3806 Å / Origin y: 20.2544 Å / Origin z: 50.5002 Å
111213212223313233
T0.1817 Å20.0826 Å2-0.0126 Å2-0.298 Å20.001 Å2--0.2412 Å2
L0.2149 °2-0.2385 °20.1547 °2-1.0206 °2-0.7749 °2--1.2961 °2
S-0.0533 Å °-0.2088 Å °0.0578 Å °0.0037 Å °0.1016 Å °-0.0416 Å °0.006 Å °-0.0867 Å °-0.0496 Å °
Refinement TLS groupSelection details: ALL

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