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- PDB-5j5v: CdiA-CT from uropathogenic Escherichia coli in complex with cogna... -

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Basic information

Entry
Database: PDB / ID: 5j5v
TitleCdiA-CT from uropathogenic Escherichia coli in complex with cognate immunity protein and CysK
Components
  • Cysteine synthase A
  • Immunity protein CdiI
  • tRNA nuclease CdiA
KeywordsTOXIN / complex / endonuclease / immunity protein
Function / homology
Function and homology information


S-carboxymethylcysteine synthase / S-carboxymethylcysteine synthase activity / cysteine synthase complex / tRNA-specific ribonuclease activity / L-cysteine desulfhydrase activity / cysteine synthase / cysteine synthase activity / other organism cell membrane / cysteine biosynthetic process from serine / amino acid biosynthetic process ...S-carboxymethylcysteine synthase / S-carboxymethylcysteine synthase activity / cysteine synthase complex / tRNA-specific ribonuclease activity / L-cysteine desulfhydrase activity / cysteine synthase / cysteine synthase activity / other organism cell membrane / cysteine biosynthetic process from serine / amino acid biosynthetic process / RNA endonuclease activity / pyridoxal phosphate binding / transferase activity / toxin activity / Hydrolases; Acting on ester bonds / host cell cytoplasm / tRNA binding / lyase activity / protein homodimerization activity / extracellular region / identical protein binding / membrane / cytosol / cytoplasm
Similarity search - Function
Immunity protein CdiI / CDI immunity proteins / Bacterial toxin 28 / Toxin CdiA-like, Filamentous hemagglutinin motif repeats / VENN motif-containing domain / Pre-toxin domain with VENN motif / Hemagglutinin repeat / Hemagglutinin repeat / Filamentous haemagglutinin FhaB/tRNA nuclease CdiA-like, TPS domain / TPS secretion domain ...Immunity protein CdiI / CDI immunity proteins / Bacterial toxin 28 / Toxin CdiA-like, Filamentous hemagglutinin motif repeats / VENN motif-containing domain / Pre-toxin domain with VENN motif / Hemagglutinin repeat / Hemagglutinin repeat / Filamentous haemagglutinin FhaB/tRNA nuclease CdiA-like, TPS domain / TPS secretion domain / haemagglutination activity domain / Cysteine synthase CysK / Cysteine synthase / Parallel beta-helix repeat / Parallel beta-helix repeats / Cysteine synthase/cystathionine beta-synthase, pyridoxal-phosphate attachment site / Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site. / : / Rossmann fold - #1100 / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pectin lyase fold / Pectin lyase fold/virulence factor / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Cysteine synthase A / Cysteine synthase A / tRNA nuclease CdiA / Immunity protein CdiI
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
Escherichia coli O6:K15:H31 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsGoulding, C.W. / Johnson, P.M. / Morse, R.P.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2016
Title: Unraveling the essential role of CysK in CDI toxin activation.
Authors: Johnson, P.M. / Beck, C.M. / Morse, R.P. / Garza-Sanchez, F. / Low, D.A. / Hayes, C.S. / Goulding, C.W.
History
DepositionApr 4, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2017Group: Database references
Revision 1.2May 3, 2017Group: Non-polymer description
Revision 1.3Sep 27, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cysteine synthase A
B: tRNA nuclease CdiA
C: Immunity protein CdiI
D: Cysteine synthase A
E: tRNA nuclease CdiA
F: Immunity protein CdiI


Theoretical massNumber of molelcules
Total (without water)151,6036
Polymers151,6036
Non-polymers00
Water1,820101
1
A: Cysteine synthase A
B: tRNA nuclease CdiA
C: Immunity protein CdiI


Theoretical massNumber of molelcules
Total (without water)75,8013
Polymers75,8013
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-23 kcal/mol
Surface area22880 Å2
MethodPISA
2
D: Cysteine synthase A
E: tRNA nuclease CdiA
F: Immunity protein CdiI


Theoretical massNumber of molelcules
Total (without water)75,8013
Polymers75,8013
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4630 Å2
ΔGint-23 kcal/mol
Surface area23000 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13740 Å2
ΔGint-60 kcal/mol
Surface area41340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.251, 195.539, 175.061
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Cysteine synthase A / CSase A / O-acetylserine (thiol)-lyase A / OAS-TL A / O-acetylserine sulfhydrylase A / Sulfate ...CSase A / O-acetylserine (thiol)-lyase A / OAS-TL A / O-acetylserine sulfhydrylase A / Sulfate starvation-induced protein 5 / SSI5


Mass: 34726.660 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: cysK, Z3680, ECs3286 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P0ABK6, UniProt: P0ABK5*PLUS, cysteine synthase
#2: Protein tRNA nuclease CdiA / tRNase CdiA / Toxin CdiA


Mass: 24841.490 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O6:K15:H31 (strain 536 / UPEC) (bacteria)
Strain: 536 / UPEC / Gene: cdiA, ECP_4580 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q0T963, Hydrolases; Acting on ester bonds
#3: Protein Immunity protein CdiI


Mass: 16233.229 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O6:K15:H31 (strain 536 / UPEC) (bacteria)
Strain: 536 / UPEC / Gene: cdiI, ECP_4579 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q0T964
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.35 Å3/Da / Density % sol: 47.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 0.1 M sodium cacodylate (pH 7.1), 0.2 M ammonium sulfate, 17% (w/v) PEG-8000

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Data collection

DiffractionMean temperature: 70 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.75→48.825 Å / Num. obs: 36681 / % possible obs: 99.97 % / Redundancy: 14.5 % / Net I/σ(I): 10.41

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
PHENIX(Phaser-MR: 1.10.1_2155)phasing
PHENIX(AutoBuild: 1.10.1_2155)model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5J43

5j43


Resolution: 2.75→48.825 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.54
RfactorNum. reflection% reflection
Rfree0.2481 914 2.49 %
Rwork0.1964 --
obs0.1976 36673 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.75→48.825 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8197 0 0 101 8298
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0118311
X-RAY DIFFRACTIONf_angle_d1.07211238
X-RAY DIFFRACTIONf_dihedral_angle_d14.4195130
X-RAY DIFFRACTIONf_chiral_restr0.0621309
X-RAY DIFFRACTIONf_plane_restr0.0071460
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.8950.34971290.27335044X-RAY DIFFRACTION100
2.895-3.07630.29011280.24765029X-RAY DIFFRACTION100
3.0763-3.31380.3021300.23525074X-RAY DIFFRACTION100
3.3138-3.64720.24691300.20715081X-RAY DIFFRACTION100
3.6472-4.17470.25091300.17775086X-RAY DIFFRACTION100
4.1747-5.25870.20481310.16325142X-RAY DIFFRACTION100
5.2587-48.83240.22061360.18015303X-RAY DIFFRACTION100

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