5T87

Crystal structure of CDI complex from Cupriavidus taiwanensis LMG 19424


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

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

  • DOI: 10.1002/prot.25392

  • 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 ...

    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

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CdiI immunity protein
A, B, C, D
116Cupriavidus taiwanensis (strain DSM 17343 / BCRC 17206 / CIP 107171 / LMG 19424 / R1)Mutation(s): 0 
Find proteins for B3R1C2 (Cupriavidus taiwanensis (strain DSM 17343 / BCRC 17206 / CIP 107171 / LMG 19424 / R1))
Go to UniProtKB:  B3R1C2
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CdiA toxin
E, F, G, H
76Cupriavidus taiwanensis (strain DSM 17343 / BCRC 17206 / CIP 107171 / LMG 19424 / R1)Mutation(s): 0 
Find proteins for B3R1C1 (Cupriavidus taiwanensis (strain DSM 17343 / BCRC 17206 / CIP 107171 / LMG 19424 / R1))
Go to UniProtKB:  B3R1C1
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E, F, G, H
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.215 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 107.097α = 90.00
b = 107.097β = 90.00
c = 315.271γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000phasing
SBC-Collectdata collection
HKL-3000data scaling
HKL-3000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM115586

Revision History 

  • Version 1.0: 2017-09-13
    Type: Initial release
  • Version 1.1: 2017-09-27
    Type: Author supporting evidence
  • Version 1.2: 2017-11-08
    Type: Database references
  • Version 1.3: 2018-02-28
    Type: Database references