1XX6

X-ray structure of Clostridium acetobutylicum thymidine kinase with ADP. Northeast Structural Genomics Target CAR26.

• PDB DOI: https://doi.org/10.2210/pdb1XX6/pdb

• Classification: TRANSFERASE
• Organism(s): Clostridium acetobutylicum ATCC 824
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2004-11-04 Released: 2004-12-21 
• Deposition Author(s): Kuzin, A.P., Abashidze, M., Forouhar, F., Vorobiev, S.M., Acton, T.B., Ma, L.-C., Xiao, R., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.266 
• R-Value Work: 0.241 
• R-Value Observed: 0.241 

Literature

X-ray structure of Clostridium acetobutylicum thymidine kinase with ADP. Northeast Structural Genomics Target CAR26.

Kuzin, A.P., Abashidze, M., Forouhar, F., Vorobiev, S.M., Acton, T.B., Ma, L.-C., Xiao, R., Montelione, G.T., Tong, L., Hunt, J.F.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 45.15 kDa 
• Atom Count: 2,988 
• Modelled Residue Count: 344 
• Deposited Residue Count: 382 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidine kinase	A, B	191	Clostridium acetobutylicum ATCC 824	Mutation(s): 5  EC: 2.7.1.21
UniProt
Find proteins for Q97F65 (Clostridium acetobutylicum (strain ATCC 824 / DSM 792 / JCM 1419 / IAM 19013 / LMG 5710 / NBRC 13948 / NRRL B-527 / VKM B-1787 / 2291 / W)) Explore Q97F65  Go to UniProtKB:  Q97F65

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	D [auth A], F [auth B]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
ZN	C [auth A], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.266 
• R-Value Work: 0.241 
• R-Value Observed: 0.241 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.793	α = 90
b = 67.166	β = 90
c = 103.638	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-12-21 
Deposition Author(s): Kuzin, A.P., Abashidze, M., Forouhar, F., Vorobiev, S.M., Acton, T.B., Ma, L.-C., Xiao, R., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2004-12-21
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2024-03-06
  Changes: Data collection, Database references, Derived calculations