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- PDB-6ijf: Crystal structure of the type VI effector-immunity complex (Tae4-... -

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Basic information

Entry
Database: PDB / ID: 6ijf
TitleCrystal structure of the type VI effector-immunity complex (Tae4-Tai4) from Agrobacterium tumefaciens
Components
  • Tae4
  • Tai4
KeywordsANTITOXIN / COMPLEX
Function / homology
Function and homology information


endopeptidase fold (from Nostoc punctiforme) - #80 / MYOD Basic-Helix-Loop-Helix Domain, subunit B - #80 / Rap1a immunity protein / Rap1a immunity proteins / Type VI secretion system (T6SS), amidase effector protein 4 / Type VI secretion system (T6SS), amidase effector protein 4 / MYOD Basic-Helix-Loop-Helix Domain, subunit B / endopeptidase fold (from Nostoc punctiforme) / Few Secondary Structures / Irregular ...endopeptidase fold (from Nostoc punctiforme) - #80 / MYOD Basic-Helix-Loop-Helix Domain, subunit B - #80 / Rap1a immunity protein / Rap1a immunity proteins / Type VI secretion system (T6SS), amidase effector protein 4 / Type VI secretion system (T6SS), amidase effector protein 4 / MYOD Basic-Helix-Loop-Helix Domain, subunit B / endopeptidase fold (from Nostoc punctiforme) / Few Secondary Structures / Irregular / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Rap1a domain-containing protein / Uncharacterized protein
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsFukuhara, S. / Nakane, T. / Yamashita, K. / Ishii, R. / Ishitani, R. / Nureki, O.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2018
Title: Crystal structure of the Agrobacterium tumefaciens type VI effector-immunity complex.
Authors: Fukuhara, S. / Nakane, T. / Yamashita, K. / Ishii, R. / Ishitani, R. / Nureki, O.
History
DepositionOct 9, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tai4
B: Tai4
C: Tae4
D: Tae4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5416
Polymers59,2064
Non-polymers3342
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8030 Å2
ΔGint-44 kcal/mol
Surface area20540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.025, 72.025, 194.348
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUCYSCYSAA2 - 995 - 102
21GLUGLUCYSCYSBB2 - 995 - 102
12METMETSERSERCC1 - 1632 - 164
22METMETSERSERDD1 - 1632 - 164

NCS ensembles :
ID
1
2

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Components

#1: Protein Tai4


Mass: 11482.844 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Gene: SY94_4314 / Plasmid: modified pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) / References: UniProt: A0A083ZID3
#2: Protein Tae4


Mass: 18120.299 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Gene: SY94_4315 / Plasmid: modified pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) / References: UniProt: A0A083ZID4
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.46 Å3/Da / Density % sol: 49.96 % / Mosaicity: 0 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 35 % PEG 400, 0.05 M Tris pH 8.5, 0.05 M sodium sulfate, 0.05 M lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Dec 16, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→97.18 Å / Num. obs: 44633 / % possible obs: 99.6 % / Redundancy: 10.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.022 / Rrim(I) all: 0.07 / Net I/σ(I): 15 / Num. measured all: 452487 / Scaling rejects: 117
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.9-1.947.31.43127680.5280.5441.53896.3
9.11-97.189.40.0414180.9990.0140.04397.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
Aimless0.5.26data scaling
PDB_EXTRACT3.24data extraction
DIALSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BI8

4bi8


Resolution: 1.9→62.38 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.964 / SU B: 4.379 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.149 / ESU R Free: 0.13 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21252 2278 5.1 %RANDOM
Rwork0.19027 ---
obs0.19142 42275 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 47.589 Å2
Baniso -1Baniso -2Baniso -3
1-0.95 Å20.47 Å20 Å2
2--0.95 Å2-0 Å2
3----3.08 Å2
Refinement stepCycle: 1 / Resolution: 1.9→62.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4036 0 21 122 4179
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0134178
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173748
X-RAY DIFFRACTIONr_angle_refined_deg1.5721.655687
X-RAY DIFFRACTIONr_angle_other_deg1.41.5798705
X-RAY DIFFRACTIONr_dihedral_angle_1_deg20.9795.426551
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.81921.643207
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.6615622
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2811528
X-RAY DIFFRACTIONr_chiral_restr0.0770.2548
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025280
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02903
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.4134.8972108
X-RAY DIFFRACTIONr_mcbond_other4.4114.8952107
X-RAY DIFFRACTIONr_mcangle_it5.6297.3152630
X-RAY DIFFRACTIONr_mcangle_other5.637.3182631
X-RAY DIFFRACTIONr_scbond_it4.9085.3312070
X-RAY DIFFRACTIONr_scbond_other4.9065.3312070
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.797.8073054
X-RAY DIFFRACTIONr_long_range_B_refined9.22992.48617414
X-RAY DIFFRACTIONr_long_range_B_other9.23592.48417358
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.01

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A29840.11
12B29840.11
21C52120.09
22D52120.09
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 140 -
Rwork0.343 3036 -
obs--96.27 %

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