5T87 | pdb_00005t87

Crystal structure of CDI complex from Cupriavidus taiwanensis LMG 19424

• PDB DOI: https://doi.org/10.2210/pdb5T87/pdb

• Classification: TOXIN
• Organism(s): Cupriavidus taiwanensis LMG 19424
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-09-06 Released: 2017-09-13 
• Deposition Author(s): 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 Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.247 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Literature

Target highlights from the first post-PSI CASP experiment (CASP12, May-August 2016).

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.

(2018) Proteins 86 Suppl 1: 27-50

• PubMed: 28960539 
• DOI: https://doi.org/10.1002/prot.25392
• Primary Citation of Related Structures:  
  5T87


• PubMed Abstract: 
  

  The functional and biological significance of the selected CASP12 targets are described by the authors of the structures. The crystallographers discuss the most interesting structural features of the target proteins and assess whether these features were correctly reproduced in the predictions submitted to the CASP12 experiment.

---

Organizational Affiliation: 
• Genome Center, University of California, Davis, 451 Health Sciences Drive, Davis, California, 95616.
Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, 72076, Germany.
Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne NE2 4HH, United Kingdom.
CIISA - Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477, Portugal, Lisboa.
Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, England, United Kingdom.
UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Cien⁁cias e Tecnologia, Universidade Nova de Lisboa, Caparica, 2829-516, Portugal.
Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, 20850.
Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel.
Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen Ø, Denmark.
Department of Molecular Biology and Biochemistry/Pharmaceutical Sciences, University of California Irvine, Irvine, California, 92697.
Department of Molecular, Cellular and Developmental Biology/Biomolecular Science and Engineering Program, University of California, Santa Barbara, Santa Barbara, California, 93106.
Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, 20742.
Argonne National Laboratory, Midwest Center for Structural Genomics/Structural Biology Center, Biosciences Division, Argonne, Illinois, 60439.
Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, 60637.
Microbiology, Saarland University, Campus Building A1.5, Saarbrücken, Saarland, D-66123, Germany.
Netherlands Centre for Electron Nanoscopy, Institute of Biology Leiden, Leiden University, 2333, CC Leiden, The Netherlands.
Department of Molecular Cell Biology, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands.
Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milano, 20126, Italy.
Department of Cell Biology and Molecular genetics, University of Maryland, 9600 Gudelsky Drive, Institute for Bioscience and Biotechnology Research, Rockville, Maryland, 20850.
Department of Biosciences, University of Milano, Milano, 20133, Italy.
Department of Macromolecular Structures, Centro Nacional de Biotecnologia (CSIC), calle Darwin 3, Madrid, 28049, Spain.
Université de Lyon, Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 - CNRS, ENS Lyon, UCB Lyon 1), Villeurbanne, 69100, France.
University of Maryland School of Medicine, Institute of Human Virology, Baltimore, Maryland, 21201.
Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Henry Wellcome Building, University Road, Leicester, LE1 7RN, UK.
School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, United Kingdom.
Department of Medicine and Department of Microbiology and Immunology, University of Maryland School of Medicine, Institute of Human Virology, Baltimore, Maryland, 21201.
Latvian Biomedical Research and Study Center, Rātsupītes 1, Riga, LV1067, Latvia.
Faculty of Biology, Department of Molecular Biology, University of Latvia, Jelgavas 1, Riga, LV-1004, Latvia.
Biozentrum/SIB Swiss Institute of Bioinformatics, Klingelbergstrasse 50, Basel, 4056, Switzerland.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 86.35 kDa 
• Atom Count: 6,002 
• Modeled Residue Count: 745 
• Deposited Residue Count: 768 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CdiI immunity protein	A, B, C, D	116	Cupriavidus taiwanensis LMG 19424	Mutation(s): 0  Gene Names: RALTA_A1586
UniProt
Find proteins for B3R1C2 (Cupriavidus taiwanensis (strain DSM 17343 / BCRC 17206 / CCUG 44338 / CIP 107171 / LMG 19424 / R1)) Explore B3R1C2  Go to UniProtKB:  B3R1C2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CdiA toxin	E, F, G, H	76	Cupriavidus taiwanensis LMG 19424	Mutation(s): 0  Gene Names: RALTA_A1585
UniProt
Find proteins for B3R1C1 (Cupriavidus taiwanensis (strain DSM 17343 / BCRC 17206 / CCUG 44338 / CIP 107171 / LMG 19424 / R1)) Explore B3R1C1  Go to UniProtKB:  B3R1C1

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.247 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m35t87

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.097	α = 90
b = 107.097	β = 90
c = 315.271	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SBC-Collect	data collection

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-09-13 
Deposition Author(s): 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 Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM115586

Revision History  

• Version 1.0: 2017-09-13
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Author supporting evidence
• Version 1.2: 2017-11-08
  Changes: Database references
• Version 1.3: 2018-02-28
  Changes: Database references
• Version 1.4: 2019-12-25
  Changes: Author supporting evidence
• Version 1.5: 2024-10-09
  Changes: Data collection, Database references, Structure summary