5T87

Crystal structure of CDI complex from Cupriavidus taiwanensis LMG 19424


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.216 

wwPDB Validation   3D Report Full Report


This is version 1.4 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: 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CdiI immunity protein
A, B, C, D
116Cupriavidus taiwanensis LMG 19424Mutation(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 Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB3R1C2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CdiA toxin
E, F, G, H
76Cupriavidus taiwanensis LMG 19424Mutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB3R1C1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.097α = 90
b = 107.097β = 90
c = 315.271γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SBC-Collectdata collection

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM115586

Revision History  (Full details and data files)

  • 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