3LD9 | pdb_00003ld9

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

• PDB DOI: https://doi.org/10.2210/pdb3LD9/pdb

• Classification: TRANSFERASE
• Organism(s): Ehrlichia chaffeensis str. Arkansas
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-01-12 Released: 2010-02-16 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.232 (Depositor), 0.249 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: experimental

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 Struct Biol Cryst Commun 67: 1090-1094

• PubMed: 21904055 
• DOI: https://doi.org/10.1107/S174430911101493X
• Primary Citation Related Structures: 
  3LD9


• 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 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.

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Organizational Affiliation: 
• Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 102.56 kDa 
• Atom Count: 6,104 
• Modeled Residue Count: 724 
• Deposited Residue Count: 892 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidylate kinase	A, B, C, D	223	Ehrlichia chaffeensis str. Arkansas	Mutation(s): 0  Gene Names: tmk, ECH_0229 EC: 2.7.4.9
UniProt
Find proteins for Q2GHN3 (Ehrlichia chaffeensis (strain ATCC CRL-10679 / Arkansas)) Explore Q2GHN3  Go to UniProtKB:  Q2GHN3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], F [auth B], H [auth C], I [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	G [auth B], J [auth D]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.232 (Depositor), 0.249 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33LD9

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.17	α = 90
b = 144.82	β = 90
c = 146.84	γ = 90

Software Package:

Software Name	Purpose
BOS	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-02-16 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2010-02-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-09-21
  Changes: Database references
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description