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- PDB-4jmf: Crystal structure of ExoT (residues 28 -77)- SpcS complex from Ps... -

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Basic information

Entry
Database: PDB / ID: 4jmf
TitleCrystal structure of ExoT (residues 28 -77)- SpcS complex from Pseudomonas aeruginosa at 2.1 angstrom
Components
  • Exoenzyme T
  • Probable chaperone
KeywordsTOXIN/CHAPERONE / Type III secretion system / T3SS / virulent effector / TOXIN-CHAPERONE complex
Function / homology
Function and homology information


NAD+-protein-arginine ADP-ribosyltransferase / NAD+-protein-arginine ADP-ribosyltransferase activity / protein secretion by the type III secretion system / NAD+ ADP-ribosyltransferase activity / nucleotidyltransferase activity / GTPase activator activity / toxin activity / extracellular region
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2690 / Type III secretion chaperone SycE / Type III secretion system effector protein YopE-like / Virulence factor YopE, GAP domain / Virulence factor YopE, GAP domain superfamily / Yersinia virulence determinant (YopE) / Tir chaperone protein (CesT) family / Tir chaperone protein (CesT) family / Yope Regulator; Chain: A, - #10 / Yope Regulator; Chain: A, ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2690 / Type III secretion chaperone SycE / Type III secretion system effector protein YopE-like / Virulence factor YopE, GAP domain / Virulence factor YopE, GAP domain superfamily / Yersinia virulence determinant (YopE) / Tir chaperone protein (CesT) family / Tir chaperone protein (CesT) family / Yope Regulator; Chain: A, - #10 / Yope Regulator; Chain: A, / ADP ribosyltransferase / ADP-ribosyltransferase exoenzyme / Toxin-related mono-ADP-ribosyltransferase (TR mART) core domain profile. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Probable chaperone / Exoenzyme T
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.099 Å
AuthorsDatta, S. / Dey, S.
CitationJournal: Febs J. / Year: 2014
Title: Interfacial residues of SpcS chaperone affects binding of effector toxin ExoT in Pseudomonas aeruginosa: novel insights from structural and computational studies
Authors: Dey, S. / Datta, S.
History
DepositionMar 14, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650HELIX Determination method: Author determined
Remark 700SHEET Determination method: Author determined

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Exoenzyme T
B: Probable chaperone
C: Probable chaperone
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8524
Polymers31,7603
Non-polymers921
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6940 Å2
ΔGint-46 kcal/mol
Surface area12830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.322, 78.322, 194.221
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-106-

HOH

21C-343-

HOH

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Components

#1: Protein/peptide Exoenzyme T


Mass: 5416.263 Da / Num. of mol.: 1 / Fragment: UNP residues 28-77
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PA01 / Gene: exoT / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9I788
#2: Protein Probable chaperone / SpcS


Mass: 13171.843 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PA01 / Gene: SpcS / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G3XD93
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.71 Å3/Da / Density % sol: 54.57 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 6.5
Details: 28% PEGMME 5000, 0.2M ammonium sulphate, pH 6.5, vapour diffusion, temperature 295K, VAPOR DIFFUSION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 5, 2012
RadiationMonochromator: Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.099→40 Å / Num. all: 21477 / Num. obs: 21244 / % possible obs: 99 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 34.09 Å2
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.09-2.26195
2.26-2.491100
2.49-2.851100
2.85-3.59199
3.59-50199

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
StructureStudiodata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MIR / Resolution: 2.099→30.482 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8389 / SU ML: 0.21 / σ(F): 0 / Phase error: 22.38 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2431 1981 9.39 %random
Rwork0.1977 ---
all0.202 21477 --
obs0.202 21090 98.25 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.32 Å2 / Biso mean: 34.0488 Å2 / Biso min: 13.29 Å2
Refinement stepCycle: LAST / Resolution: 2.099→30.482 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2231 0 6 134 2371
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072283
X-RAY DIFFRACTIONf_angle_d1.1723101
X-RAY DIFFRACTIONf_chiral_restr0.08344
X-RAY DIFFRACTIONf_plane_restr0.005419
X-RAY DIFFRACTIONf_dihedral_angle_d15.737869
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0986-2.15110.34641190.32491099121882
2.1511-2.20920.26611320.26471290142295
2.2092-2.27420.31971390.24111340147999
2.2742-2.34760.25461410.214713611502100
2.3476-2.43150.28141400.204413501490100
2.4315-2.52880.28171430.210513771520100
2.5288-2.64380.24881400.202713441484100
2.6438-2.78310.24111430.200713821525100
2.7831-2.95740.23251420.202813781520100
2.9574-3.18550.23191430.206213761519100
3.1855-3.50560.27021450.199614001545100
3.5056-4.01190.21321470.184314181565100
4.0119-5.05090.22041480.161714431591100
5.0509-30.48550.2291590.19331551171099

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