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

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Basic information

Entry
Database: PDB / ID: 4hfk
TitleCrystal structure of the type VI effector-immunity complex Tae4-Tai4 from Enterobacter cloacae
Components
  • Putative cytoplasmic proteinCytoplasm
  • Putative uncharacterized 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
Putative cytoplasmic protein / Uncharacterized protein / Putative cytoplasmic protein / Uncharacterized protein
Similarity search - Component
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 8, 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

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Assembly

Deposited unit
A: Putative cytoplasmic protein
B: Putative uncharacterized protein
C: Putative cytoplasmic protein
D: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8285
Polymers61,7324
Non-polymers961
Water8,593477
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6890 Å2
ΔGint-49 kcal/mol
Surface area21090 Å2
MethodPISA
2
A: Putative cytoplasmic protein
B: Putative uncharacterized protein
C: Putative cytoplasmic protein
D: Putative uncharacterized protein
hetero molecules

A: Putative cytoplasmic protein
B: Putative uncharacterized protein
C: Putative cytoplasmic protein
D: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,65710
Polymers123,4658
Non-polymers1922
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area16140 Å2
ΔGint-119 kcal/mol
Surface area39810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.342, 138.144, 64.462
Angle α, β, γ (deg.)90.00, 127.89, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-318-

HOH

21B-337-

HOH

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Components

#1: Protein Putative cytoplasmic protein / Cytoplasm


Mass: 19165.059 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter cloacae (bacteria) / Strain: ATCC 13047 / DSM 30054 / NBRC 13535 / NCDC 279-56 / Gene: ECL_01542 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D5C6F6, UniProt: A0A0H3CIJ2*PLUS
#2: Protein Putative uncharacterized protein


Mass: 11701.106 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 19-117
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter cloacae (bacteria) / Strain: ATCC 13047 / DSM 30054 / NBRC 13535 / NCDC 279-56 / Gene: ECL_01543 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D5C6F7, UniProt: A0A0H3CIX8*PLUS
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 477 / 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: 2.6 Å3/Da / Density % sol: 52.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M Sodium chloride, 0.1M Na/K phosphate pH 6.5, 25% (w/v) PEG 1000, 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 18, 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: 2.1→50 Å / Num. all: 36726 / Num. obs: 36726 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 34.5
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.232 / Mean I/σ(I) obs: 10.5 / Num. unique all: 1834 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4HFF

4hff


Resolution: 2.1→23.402 Å / SU ML: 0.24 / σ(F): 1.35 / Phase error: 18.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2035 1834 5 %RANDOM
Rwork0.1568 ---
all0.1591 36681 --
obs0.1568 36681 99.96 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.486 Å2 / ksol: 0.401 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.7697 Å2-0 Å2-1.0899 Å2
2---2.4582 Å20 Å2
3---0.6885 Å2
Refinement stepCycle: LAST / Resolution: 2.1→23.402 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3934 0 5 477 4416
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074042
X-RAY DIFFRACTIONf_angle_d1.0575481
X-RAY DIFFRACTIONf_dihedral_angle_d12.5951445
X-RAY DIFFRACTIONf_chiral_restr0.071606
X-RAY DIFFRACTIONf_plane_restr0.005706
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.1-2.15680.24551380.17452675
2.1568-2.22020.21321630.15022645
2.2202-2.29180.21661240.14262678
2.2918-2.37360.20311440.14422679
2.3736-2.46850.21611290.15142695
2.4685-2.58080.22141360.15172678
2.5808-2.71660.22291360.15912666
2.7166-2.88660.19011520.15882683
2.8866-3.1090.2071260.16122681
3.109-3.4210.21041400.16632693
3.421-3.9140.19161460.15462688
3.914-4.92360.16731460.1352676
4.9236-23.40390.21021540.1862710

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