+Open data
-Basic information
Entry | Database: PDB / ID: 5j43 | ||||||
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Title | CdiA-CT from uropathogenic Escherichia coli in complex with CysK | ||||||
Components |
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Keywords | TOXIN / complex / endonuclease | ||||||
Function / homology | Function and homology information S-carboxymethylcysteine synthase / S-carboxymethylcysteine synthase activity / tRNA-specific ribonuclease activity / cysteine synthase complex / 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 / tRNA-specific ribonuclease activity / cysteine synthase complex / 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 / toxin activity / transferase activity / host cell cytoplasm / tRNA binding / Hydrolases; Acting on ester bonds / lyase activity / protein homodimerization activity / extracellular region / membrane / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli O157:H7 (bacteria) Escherichia coli O6:K15:H31 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Morse, R.P. / Goulding, C.W. / Johnson, P.M. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5j43.cif.gz | 173.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5j43.ent.gz | 132.2 KB | Display | PDB format |
PDBx/mmJSON format | 5j43.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j4/5j43 ftp://data.pdbj.org/pub/pdb/validation_reports/j4/5j43 | HTTPS FTP |
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-Related structure data
Related structure data | 5j5vC 1oasS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 | 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 / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.09 Å3/Da / Density % sol: 60.24 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 70 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 15, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→64.01 Å / Num. obs: 39863 / % possible obs: 99.4 % / Redundancy: 12.8 % / Net I/σ(I): 9.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→44.919 Å
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Refine LS restraints |
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LS refinement shell |
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