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Yorodumi- PDB-5t87: Crystal structure of CDI complex from Cupriavidus taiwanensis LMG... -
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-Basic information
Entry | Database: PDB / ID: 5t87 | ||||||
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Title | Crystal structure of CDI complex from Cupriavidus taiwanensis LMG 19424 | ||||||
Components |
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Keywords | TOXIN / Contact-dependent growth inhibition / antitoxin / immunity protein / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / Structure-Function Analysis of Polymorphic CDI Toxin-Immunity Protein Complexes / UC4CDI | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Cupriavidus taiwanensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å | ||||||
Authors | Michalska, K. / Joachimiak, G. / Jedrzejczak, R. / Hayes, C.S. / Goulding, C.W. / Joachimiak, A. / Structure-Function Analysis of Polymorphic CDI Toxin-Immunity Protein Complexes (UC4CDI) / Midwest Center for Structural Genomics (MCSG) | ||||||
Funding support | United States, 1items
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Citation | Journal: Proteins / Year: 2018 Title: Target highlights from the first post-PSI CASP experiment (CASP12, May-August 2016). Authors: Kryshtafovych, A. / Albrecht, R. / Basle, A. / Bule, P. / Caputo, A.T. / Carvalho, A.L. / Chao, K.L. / Diskin, R. / Fidelis, K. / Fontes, C.M.G.A. / Fredslund, F. / Gilbert, H.J. / Goulding, ...Authors: Kryshtafovych, A. / Albrecht, R. / Basle, A. / Bule, P. / Caputo, A.T. / Carvalho, A.L. / Chao, K.L. / Diskin, R. / Fidelis, K. / Fontes, C.M.G.A. / Fredslund, F. / Gilbert, H.J. / Goulding, C.W. / Hartmann, M.D. / Hayes, C.S. / Herzberg, O. / Hill, J.C. / Joachimiak, A. / Kohring, G.W. / Koning, R.I. / Lo Leggio, L. / Mangiagalli, M. / Michalska, K. / Moult, J. / Najmudin, S. / Nardini, M. / Nardone, V. / Ndeh, D. / Nguyen, T.H. / Pintacuda, G. / Postel, S. / van Raaij, M.J. / Roversi, P. / Shimon, A. / Singh, A.K. / Sundberg, E.J. / Tars, K. / Zitzmann, N. / Schwede, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5t87.cif.gz | 297 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5t87.ent.gz | 257.6 KB | Display | PDB format |
PDBx/mmJSON format | 5t87.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5t87_validation.pdf.gz | 473.4 KB | Display | wwPDB validaton report |
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Full document | 5t87_full_validation.pdf.gz | 476.6 KB | Display | |
Data in XML | 5t87_validation.xml.gz | 26.6 KB | Display | |
Data in CIF | 5t87_validation.cif.gz | 38.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t8/5t87 ftp://data.pdbj.org/pub/pdb/validation_reports/t8/5t87 | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 13100.101 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cupriavidus taiwanensis (strain DSM 17343 / BCRC 17206 / CIP 107171 / LMG 19424 / R1) (bacteria) Strain: DSM 17343 / BCRC 17206 / CIP 107171 / LMG 19424 / R1 Gene: RALTA_A1586 / Plasmid: pMCSG81 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B3R1C2 #2: Protein | Mass: 8487.235 Da / Num. of mol.: 4 / Fragment: catalytic domain Source method: isolated from a genetically manipulated source Details: The cloned fragment is longer and starts with T3228 of the original sequence, however purified complex was treated with trypsin prior to crystallization. The provided sequence corresponds to ...Details: The cloned fragment is longer and starts with T3228 of the original sequence, however purified complex was treated with trypsin prior to crystallization. The provided sequence corresponds to the most likely fragment obtained after cleavage. Source: (gene. exp.) Cupriavidus taiwanensis (strain DSM 17343 / BCRC 17206 / CIP 107171 / LMG 19424 / R1) (bacteria) Strain: DSM 17343 / BCRC 17206 / CIP 107171 / LMG 19424 / R1 Gene: RALTA_A1585 / Plasmid: pMCSG81 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B3R1C1 #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: 3.06 Å3/Da / Density % sol: 59.74 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 0.1 M Mg acetate, 0.1 M Na acetate, 8% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9791519 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 24, 2014 / Details: mirrors |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791519 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→30 Å / Num. obs: 42464 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / CC1/2: 0.894 / Rmerge(I) obs: 0.143 / Net I/σ(I): 12.84 |
Reflection shell | Resolution: 2.4→2.44 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.693 / Mean I/σ(I) obs: 1.45 / % possible all: 96.3 |
-Processing
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Refinement | Method to determine structure: SAD / Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.922 / SU B: 20.794 / SU ML: 0.22 / Cross valid method: THROUGHOUT / ESU R: 0.311 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.62 Å2
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Refinement step | Cycle: 1 / Resolution: 2.4→30 Å
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Refine LS restraints |
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