3HJN | pdb_00003hjn

Crystal structure of thymidylate kinase in complex with dTDP and ADP from Thermotoga maritima

• PDB DOI: https://doi.org/10.2210/pdb3HJN/pdb
• Entry: 3HJN supersedes: 2Z0H

• Classification: TRANSFERASE
• Organism(s): Thermotoga maritima MSB8
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-05-22 Released: 2009-06-02 
• Deposition Author(s): Yoshikawa, S., Nakagawa, N., Shirouzu, M., Yokoyama, S., Kuramitsu, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.285 (Depositor), 0.285 (DCC) 
• R-Value Work: 
  0.226 (Depositor), 0.225 (DCC) 

Starting Model: experimental

Literature

Crystal structure of thymidylate kinase in complex with dTDP and ADP from Thermotoga maritima

Yoshikawa, S., Nakagawa, N., Shirouzu, M., Yokoyama, S., Kuramitsu, 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: 47.45 kDa 
• Atom Count: 3,202 
• Modeled Residue Count: 373 
• Deposited Residue Count: 394 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidylate kinase	A, B	197	Thermotoga maritima MSB8	Mutation(s): 0  Gene Names: tmk, TM_1099 EC: 2.7.4.9
UniProt
Find proteins for Q9X0I3 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X0I3  Go to UniProtKB:  Q9X0I3

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	C [auth A], F [auth B]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
TYD	D [auth A], G [auth B]	THYMIDINE-5'-DIPHOSPHATE C10 H16 N2 O11 P2 UJLXYODCHAELLY-XLPZGREQSA-N
MG	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.285 (Depositor), 0.285 (DCC) 
• R-Value Work:  0.226 (Depositor), 0.225 (DCC) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.587	α = 90
b = 127.05	β = 90
c = 133.519	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-06-02 
Deposition Author(s): Yoshikawa, S., Nakagawa, N., Shirouzu, M., Yokoyama, S., Kuramitsu, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)
• This entry supersedes: 2Z0H

Revision History  

• Version 1.0: 2009-06-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description