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- PDB-5ako: The complex of Tse2 and Tsi2 from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 5ako
TitleThe complex of Tse2 and Tsi2 from Pseudomonas aeruginosa
Components
  • TSE2
  • TSI2
KeywordsUNKNOWN FUNCTION / T6SS / IMMUNITY PROTEIN / TOXIN
Function / homology
Function and homology information


extracellular region
Similarity search - Function
Tse2 ADP-ribosyltransferase toxin / Tse2 ADP-ribosyltransferase toxin / Helix Hairpins - #2500 / Tse2 immunity protein Tsi2 / : / : / T6SS, Immune protein Tsi2-like / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Immune protein Tsi2 / Toxin Tse2
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsRobb, C.S. / Nano, F.E. / Boraston, A.B.
CitationJournal: Structure / Year: 2016
Title: The Structure of the Toxin and Type Six Secretion System Substrate Tse2 in Complex with its Immunity Protein.
Authors: Robb, C.S. / Robb, M. / Nano, F.E. / Boraston, A.B.
History
DepositionMar 4, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2016Group: Database references
Revision 1.2Mar 2, 2016Group: Database references
Revision 1.3Aug 23, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.4Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TSI2
B: TSI2
C: TSE2
D: TSE2


Theoretical massNumber of molelcules
Total (without water)57,0164
Polymers57,0164
Non-polymers00
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6710 Å2
ΔGint-34.9 kcal/mol
Surface area21360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.725, 103.138, 114.642
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TSI2


Mass: 8524.471 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9I0D9
#2: Protein TSE2


Mass: 19983.490 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9I0E0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.14 Å3/Da / Density % sol: 43 % / Description: NONE
Crystal growpH: 8 / Details: 20 MM TRIS PH 8.5, 0.2 M NACL, 22% PEG 4K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 15, 2013 / Details: K-B FOCUSING MIRRORS
RadiationMonochromator: LIQUID NITROGEN-COOLED DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→35.84 Å / Num. obs: 17725 / % possible obs: 97.6 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 35.8 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.4
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 2.3 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5refinement
XDSdata reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3VPV

3vpv


Resolution: 2.4→35.83 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.913 / SU B: 6.182 / SU ML: 0.149 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.253 896 5.1 %RANDOM
Rwork0.197 ---
obs0.2 16778 96.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.87 Å2
Baniso -1Baniso -2Baniso -3
1--6.81 Å20 Å20 Å2
2---2.66 Å20 Å2
3---9.46 Å2
Refinement stepCycle: LAST / Resolution: 2.4→35.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3437 0 0 74 3511
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0193510
X-RAY DIFFRACTIONr_bond_other_d0.0050.023257
X-RAY DIFFRACTIONr_angle_refined_deg1.5431.9834790
X-RAY DIFFRACTIONr_angle_other_deg1.0237455
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8755449
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.79324.125160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.2115515
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4221526
X-RAY DIFFRACTIONr_chiral_restr0.0850.2534
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214071
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02773
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 63 -
Rwork0.237 1239 -
obs--98.79 %

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