3LD9

Crystal structure of thymidylate kinase from Ehrlichia chaffeensis at 2.15A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of thymidylate kinase from Ehrlichia chaffeensis.

Leibly, D.J.Abendroth, J.Bryan, C.M.Sankaran, B.Kelley, A.Barrett, L.K.Stewart, L.Van Voorhis, W.C.

(2011) Acta Crystallogr.,Sect.F 67: 1090-1094

  • DOI: 10.1107/S174430911101493X

  • PubMed Abstract: 
  • The enzyme thymidylate kinase phosphorylates the substrate thymidine 5'-phosphate (dTMP) to form thymidine 5'-diphosphate (dTDP), which is further phosphorylated to dTTP for incorporation into DNA. Ehrlichia chaffeensis is the etiologic agent of huma ...

    The enzyme thymidylate kinase phosphorylates the substrate thymidine 5'-phosphate (dTMP) to form thymidine 5'-diphosphate (dTDP), which is further phosphorylated to dTTP for incorporation into DNA. Ehrlichia chaffeensis is the etiologic agent of human monocytotropic erlichiosis (HME), a potentially life-threatening tick-borne infection. HME is endemic in the United States from the southern states up to the eastern seaboard. HME is transmitted to humans via the lone star tick Amblyomma americanum. Here, the 2.15 Å resolution crystal structure of thymidylate kinase from E. chaffeensis in the apo form is presented.


    Organizational Affiliation

    Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thymidylate kinase
A, B, C, D
223Ehrlichia chaffeensis (strain ATCC CRL-10679 / Arkansas)Mutation(s): 0 
Gene Names: tmk
EC: 2.7.4.9
Find proteins for Q2GHN3 (Ehrlichia chaffeensis (strain ATCC CRL-10679 / Arkansas))
Go to UniProtKB:  Q2GHN3
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
B, D
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 39.170α = 90.00
b = 144.820β = 90.00
c = 146.840γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
BOSdata collection
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-02-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2011-09-21
    Type: Database references