4DHK

Crystal structure of a deoxycytidine triphosphate deaminase (dCTP deaminase) from Burkholderia thailandensis

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.168 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Combining functional and structural genomics to sample the essential Burkholderia structome.

Baugh, L., Gallagher, L.A., Patrapuvich, R., Clifton, M.C., Gardberg, A.S., Edwards, T.E., Armour, B., Begley, D.W., Dieterich, S.H., Dranow, D.M., Abendroth, J., Fairman, J.W., Fox, D., Staker, B.L., Phan, I., Gillespie, A., Choi, R., Nakazawa-Hewitt, S., Nguyen, M.T., Napuli, A., Barrett, L., Buchko, G.W., Stacy, R., Myler, P.J., Stewart, L.J., Manoil, C., Van Voorhis, W.C.

(2013) PLoS One 8: e53851-e53851

  • DOI: https://doi.org/10.1371/journal.pone.0053851
  • Primary Citation of Related Structures:  
    3D63, 3DAH, 3EIZ, 3EJ2, 3EK2, 3EZO, 3F0F, 3FTP, 3GK0, 3GK3, 3GVF, 3GWA, 3GWE, 3IML, 3SZ8, 3T4C, 3TML, 3TMQ, 3TXY, 3U7J, 3UE9, 3UK1, 3UK2, 3UND, 3UPT, 3URR, 3UW1, 3UW2, 3UW3, 3V2I, 3V7N, 3V8H, 3V9O, 3V9P, 3VAV, 4DDO, 4DFE, 4DHE, 4DHK, 4DUT, 4DZ4, 4E4T, 4EFI, 4EG0, 4EGJ, 4EK2, 4EQY, 4EWG, 4EXQ, 4F2G

  • PubMed Abstract: 

    • The genus Burkholderia includes pathogenic gram-negative bacteria that cause melioidosis, glanders, and pulmonary infections of patients with cancer and cystic fibrosis. Drug resistance has made development of new antimicrobials critical. Many approaches to discovering new antimicrobials, such as structure-based drug design and whole cell phenotypic screens followed by lead refinement, require high-resolution structures of proteins essential to the parasite ...

    The genus Burkholderia includes pathogenic gram-negative bacteria that cause melioidosis, glanders, and pulmonary infections of patients with cancer and cystic fibrosis. Drug resistance has made development of new antimicrobials critical. Many approaches to discovering new antimicrobials, such as structure-based drug design and whole cell phenotypic screens followed by lead refinement, require high-resolution structures of proteins essential to the parasite.

    Organizational Affiliation: 

    Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Deoxycytidine triphosphate deaminase
A, B
191Burkholderia thailandensis E264Mutation(s): 0 
Gene Names: dcd, BTH_I0860
EC: 3.5.4.13
UniProt
Find proteins for Q2T083 (Burkholderia thailandensis (strain ATCC 700388 / DSM 13276 / CCUG 48851 / CIP 106301 / E264))
Explore Q2T083 
Go to UniProtKB:  Q2T083
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2T083
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.168 
  • Space Group: H 3
  • Diffraction Data: https://doi.org/10.18430/M34DHK
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.87α = 90
b = 92.87β = 90
c = 137.59γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
XDSdata reduction

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-03-14
    Type: Initial release
  • Version 1.1: 2013-10-30
    Changes: Database references
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description