3V2I

Structure of a Peptidyl-tRNA hydrolase (PTH) from Burkholderia thailandensis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 

wwPDB Validation   3D Report Full Report


This is version 1.1 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: 10.1371/journal.pone.0053851
  • Primary Citation of Related Structures:  
    3EJ2, 3EK2, 3EIZ, 3F0F, 3EZO, 3FTP, 3GK0, 3GK3, 3IML, 3T4C, 3SZ8, 4H3Y, 4H3Z, 4H4G, 4F4H, 4F7D, 4EWG, 4EXQ, 4FK8, 4G1K, 4FRY, 4G67, 4GHK, 3GWA, 3GVF, 3GWE, 3V2I, 3UPT, 3URR, 3V7N, 3UW1, 3UW2, 3UW3, 3V8H, 3UE9, 3UK1, 3UK2, 3UND, 3V9O, 3V9P, 3VAV, 3DAH, 3TML, 3TMQ, 3U7J, 3TXY, 4DDO, 4DFE, 4DHK, 4DHE

  • 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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Peptidyl-tRNA hydrolaseA222Burkholderia thailandensis E264Mutation(s): 0 
Gene Names: pthBTH_I0472
EC: 3.1.1.29
UniProt
Find proteins for Q2T1B9 (Burkholderia thailandensis (strain ATCC 700388 / DSM 13276 / CIP 106301 / E264))
Explore Q2T1B9 
Go to UniProtKB:  Q2T1B9
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download Ideal Coordinates CCD File 
B [auth A]CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
UNL
Query on UNL

Download Ideal Coordinates CCD File 
C [auth A]Unknown ligand
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.34α = 90
b = 93.58β = 90
c = 106.76γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-01-11
    Type: Initial release
  • Version 1.1: 2013-11-13
    Changes: Database references