5H70 | pdb_00005h70

Crystal structure of ADP bound dTMP kinase (st1543) from Sulfolobus Tokodaii Strain7

• PDB DOI: https://doi.org/10.2210/pdb5H70/pdb
• Entry: 5H70 supersedes: 4RZU

• Classification: TRANSFERASE
• Organism(s): Sulfurisphaera tokodaii str. 7
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-11-15 Released: 2016-12-07 
• Deposition Author(s): Biswas, A., Jeyakanthan, J., Sekar, K., Kuramitsu, S., Yokoyama, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.300 (Depositor), 0.300 (DCC) 
• R-Value Work: 
  0.233 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.236 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of ADP bound dTMP kinase (st1543) from Sulfolobus Tokodaii Strain7

Biswas, A., Jeyakanthan, J., Sekar, K., Kuramitsu, S., Yokoyama, S.

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)

Macromolecule Content 

• Total Structure Weight: 50.44 kDa 
• Atom Count: 3,201 
• Modeled Residue Count: 412 
• Deposited Residue Count: 426 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable thymidylate kinase	A [auth B], B [auth A]	213	Sulfurisphaera tokodaii str. 7	Mutation(s): 0  Gene Names: tmk, STK_15430 EC: 2.7.4.9
UniProt
Find proteins for Q970Q8 (Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)) Explore Q970Q8  Go to UniProtKB:  Q970Q8

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	C [auth B], F [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
PGE	H [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
EDO	D [auth B], G [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	E [auth B], I [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.300 (Depositor), 0.300 (DCC) 
• R-Value Work:  0.233 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.236 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.171	α = 90
b = 63.799	β = 90
c = 141.758	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-12-07 
Deposition Author(s): Biswas, A., Jeyakanthan, J., Sekar, K., Kuramitsu, S., Yokoyama, S.
• This entry supersedes: 4RZU

Revision History  

• Version 1.0: 2016-12-07
  Type: Initial release
  
• Version 1.1: 2020-02-26
  Changes: Data collection
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description