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- PDB-4hfl: Crystal structure of the type VI effector Tae4 from Enterobacter ... -

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Basic information

Entry
Database: PDB / ID: 4hfl
TitleCrystal structure of the type VI effector Tae4 from Enterobacter cloacae
ComponentsPutative cytoplasmic proteinCytoplasm
KeywordsHYDROLASE / amidase
Function / homologyendopeptidase fold (from Nostoc punctiforme) - #70 / Type VI secretion system (T6SS), amidase effector protein 4 / Type VI secretion system (T6SS), amidase effector protein 4 / endopeptidase fold (from Nostoc punctiforme) / Alpha-Beta Complex / Alpha Beta / Putative cytoplasmic protein / Putative cytoplasmic protein
Function and homology information
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.002 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 / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative cytoplasmic protein


Theoretical massNumber of molelcules
Total (without water)19,1651
Polymers19,1651
Non-polymers00
Water1,76598
1


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

A: Putative cytoplasmic protein


Theoretical massNumber of molelcules
Total (without water)38,3302
Polymers38,3302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Buried area1230 Å2
ΔGint-11 kcal/mol
Surface area15170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.283, 84.283, 43.452
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Putative cytoplasmic protein / Cytoplasm


Mass: 19165.059 Da / Num. of mol.: 1
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.32 Å3/Da / Density % sol: 47.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.5M Ammonium sulfate, 0.1M Sodium citrate tribasic dehydrate pH5.6, 1.0M Lithium sulfate monohydrate, 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 20, 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→50 Å / Num. all: 12215 / Num. obs: 12215 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 44.3
Reflection shellResolution: 2→2.03 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.142 / Mean I/σ(I) obs: 11.1 / Num. unique all: 593 / % possible all: 98.5

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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: 2.002→23.29 Å / SU ML: 0.26 / σ(F): 1.34 / Phase error: 24.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2512 578 4.76 %RANDOM
Rwork0.2084 ---
all0.2105 12134 --
obs0.2084 12134 98.89 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.544 Å2 / ksol: 0.366 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.1234 Å2-0 Å2-0 Å2
2--4.1234 Å20 Å2
3----8.2468 Å2
Refinement stepCycle: LAST / Resolution: 2.002→23.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1229 0 0 98 1327
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091275
X-RAY DIFFRACTIONf_angle_d1.1361727
X-RAY DIFFRACTIONf_dihedral_angle_d12.587449
X-RAY DIFFRACTIONf_chiral_restr0.083186
X-RAY DIFFRACTIONf_plane_restr0.004220
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0015-2.20280.31091590.2202282998
2.2028-2.52120.29911370.231285099
2.5212-3.17520.22341490.20292902100
3.1752-23.29190.23661330.2013297599
Refinement TLS params.Method: refined / Origin x: 4.2922 Å / Origin y: -33.864 Å / Origin z: 3.2202 Å
111213212223313233
T0.0802 Å2-0.0727 Å2-0.019 Å2-0.2113 Å20.0382 Å2--0.1234 Å2
L1.2161 °2-0.2312 °20.5572 °2-1.1359 °20.1509 °2--1.8672 °2
S0.0026 Å °-0.1741 Å °-0.0414 Å °0.0043 Å °0.0398 Å °0.1156 Å °-0.1296 Å °-0.4242 Å °-0.0123 Å °
Refinement TLS groupSelection details: ALL

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