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- PDB-4j32: Structure of the effector - immunity system Tae4 / Tai4 from Salm... -

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Basic information

Entry
Database: PDB / ID: 4j32
TitleStructure of the effector - immunity system Tae4 / Tai4 from Salmonella typhimurium
Components
  • Putative cytoplasmic proteinCytoplasm
  • Putative periplasmic proteinPeriplasm
KeywordsTOXIN/INHIBITOR / N1pC/P60 papain like cysteine peptidase Tae4 / peptidoglycan hydrolase / immunity protein Tai4 / Tae4: cytoplasmatic / Tai4: periplasmatic / TOXIN-INHIBITOR complex
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
2-ETHOXYETHANOL / CITRATE ANION / Periplasmic protein / Cytoplasmic protein
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / rigid-body refinement / Resolution: 1.8 Å
AuthorsBenz, J. / Reinstein, J. / Meinhart, A.
CitationJournal: Plos One / Year: 2013
Title: Structural Insights into the Effector - Immunity System Tae4/Tai4 from Salmonella typhimurium.
Authors: Benz, J. / Reinstein, J. / Meinhart, A.
History
DepositionFeb 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Jan 15, 2014Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,17912
Polymers31,0802
Non-polymers1,09910
Water3,639202
1
A: Putative cytoplasmic protein
B: Putative periplasmic protein
hetero molecules

A: Putative cytoplasmic protein
B: Putative periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,35924
Polymers62,1604
Non-polymers2,19820
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area11780 Å2
ΔGint16 kcal/mol
Surface area23280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.650, 63.650, 365.650
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 / Cytoplasm / Tae4


Mass: 19369.020 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: Q93IS4
#2: Protein Putative periplasmic protein / Periplasm / Tai4


Mass: 11711.182 Da / Num. of mol.: 1
Fragment: periplasmatic inhibitor domain (UNP residues 27-127)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: Q8ZRL5
#3: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#4: Chemical
ChemComp-ETX / 2-ETHOXYETHANOL / 2-Ethoxyethanol


Mass: 90.121 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H10O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O

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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: 3.44 Å3/Da / Density % sol: 64.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 200 mM tri-sodium citrate pH 6.0, 30 % (v/v) 2-ethoxyethanol , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99981 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 5, 2012 / Details: Dynamically bendable mirror
RadiationMonochromator: LN2 cooled fixed-exit Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99981 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. all: 42126 / Num. obs: 42126 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 18.1 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 18.7
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 19 % / Rmerge(I) obs: 0.661 / Mean I/σ(I) obs: 4.7 / Num. unique all: 6089 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
REFMAC5.2.0019phasing
RefinementMethod to determine structure: rigid-body refinement
Starting model: 4J30

4j30


Resolution: 1.8→37.9 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.393 / SU ML: 0.056 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20332 2107 5 %RANDOM
Rwork0.18186 ---
obs0.18291 42126 99.1 %-
all-42126 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.896 Å2
Baniso -1Baniso -2Baniso -3
1-1.23 Å20.62 Å20 Å2
2--1.23 Å20 Å2
3----1.85 Å2
Refinement stepCycle: LAST / Resolution: 1.8→37.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2042 0 74 202 2318
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222257
X-RAY DIFFRACTIONr_angle_refined_deg1.4751.9633062
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.075290
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.74224.571105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.57115385
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8911511
X-RAY DIFFRACTIONr_chiral_restr0.140.2329
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021716
X-RAY DIFFRACTIONr_nbd_refined0.20.21071
X-RAY DIFFRACTIONr_nbtor_refined0.3020.21531
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1090.2171
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.285
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1420.238
X-RAY DIFFRACTIONr_mcbond_it0.7241.51380
X-RAY DIFFRACTIONr_mcangle_it1.18222178
X-RAY DIFFRACTIONr_scbond_it1.92131011
X-RAY DIFFRACTIONr_scangle_it2.954.5866
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 151 -
Rwork0.222 2857 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.47-0.59271.2482.9275-0.651.8109-0.0364-0.0303-0.0151-0.00510.05470.0732-0.0867-0.0393-0.0183-0.0332-0.0188-0.0229-0.1927-0.0025-0.136535.778936.15672.4177
20.9512-0.42210.83071.1082-0.22583.3016-0.0822-0.15470.0509-0.04450.098-0.0155-0.138-0.1076-0.0157-0.13070.05090.0251-0.15-0.004-0.150146.833330.764337.9821
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 161
2X-RAY DIFFRACTION2B27 - 127

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