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- PDB-5j43: CdiA-CT from uropathogenic Escherichia coli in complex with CysK -

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Basic information

Entry
Database: PDB / ID: 5j43
TitleCdiA-CT from uropathogenic Escherichia coli in complex with CysK
Components
  • Cysteine synthase A
  • tRNA nuclease CdiA
KeywordsTOXIN / complex / endonuclease
Function / homology
Function and homology information


S-carboxymethylcysteine synthase / S-carboxymethylcysteine synthase activity / cysteine synthase complex / tRNA-specific ribonuclease activity / cysteine synthase / L-cysteine desulfhydrase activity / 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 / cysteine synthase / L-cysteine desulfhydrase activity / 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
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 ...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 / Pectin lyase fold / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / 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
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
Escherichia coli O6:K15:H31 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsMorse, R.P. / Goulding, C.W. / Johnson, P.M.
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
DepositionMar 31, 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

Downloads & links

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Assembly

Deposited unit
E: Cysteine synthase A
F: tRNA nuclease CdiA
A: Cysteine synthase A
B: tRNA nuclease CdiA


Theoretical massNumber of molelcules
Total (without water)120,7674
Polymers120,7674
Non-polymers00
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9720 Å2
ΔGint-46 kcal/mol
Surface area31230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.010, 64.010, 365.370
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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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: 25656.768 Da / Num. of mol.: 2 / Mutation: H190A
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 3.09 Å3/Da / Density % sol: 60.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.2 M sodium sulfate, 0.1 M bis-tris propane, pH 7.9, 20% PEG 3350

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Data collection

DiffractionMean temperature: 70 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→64.01 Å / Num. obs: 39863 / % possible obs: 99.4 % / Redundancy: 12.8 % / Net I/σ(I): 9.9

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
iMOSFLM(iMosflm: 7.2.1)data 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: 1OAS

1oas


Resolution: 2.7→44.919 Å / SU ML: 0.3 / Cross valid method: NONE / σ(F): 1.38 / Phase error: 26.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2242 1978 4.99 %
Rwork0.2004 --
obs0.2016 39640 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→44.919 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6220 0 0 110 6330
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096298
X-RAY DIFFRACTIONf_angle_d1.2258513
X-RAY DIFFRACTIONf_dihedral_angle_d13.0142375
X-RAY DIFFRACTIONf_chiral_restr0.047991
X-RAY DIFFRACTIONf_plane_restr0.0081106
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7001-2.76760.31071360.30192673X-RAY DIFFRACTION98
2.7676-2.84240.36031380.27492647X-RAY DIFFRACTION99
2.8424-2.9260.33291450.25562739X-RAY DIFFRACTION99
2.926-3.02040.25411390.25432660X-RAY DIFFRACTION99
3.0204-3.12840.30361310.24742678X-RAY DIFFRACTION99
3.1284-3.25360.26481340.24292698X-RAY DIFFRACTION99
3.2536-3.40160.23571410.22362707X-RAY DIFFRACTION99
3.4016-3.58090.26731410.20812687X-RAY DIFFRACTION99
3.5809-3.80510.22651440.19682693X-RAY DIFFRACTION99
3.8051-4.09870.20041420.18752704X-RAY DIFFRACTION100
4.0987-4.51090.19591450.17122719X-RAY DIFFRACTION99
4.5109-5.16280.18041520.16172678X-RAY DIFFRACTION100
5.1628-6.50140.19291420.1952677X-RAY DIFFRACTION98
6.5014-44.92480.17881480.16082702X-RAY DIFFRACTION99

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