4RZX | pdb_00004rzx

Crystal structure (type-3) of dTMP kinase (st1543) from Sulfolobus Tokodaii Strain7

• PDB DOI: https://doi.org/10.2210/pdb4RZX/pdb

• Classification: TRANSFERASE
• Organism(s): Sulfurisphaera tokodaii str. 7
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-12-26 Released: 2015-12-30 
• Deposition Author(s): Biswas, A., Jeyakanthan, J., Sekar, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.259 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: experimental

Literature

Crystal structure (type-3) of dTMP kinase (st1543) from Sulfolobus Tokodaii Strain7

Biswas, A., Jeyakanthan, J., Sekar, K.

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: 49.51 kDa 
• Atom Count: 3,172 
• Modeled Residue Count: 406 
• Deposited Residue Count: 426 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable thymidylate kinase	A, B	213	Sulfurisphaera tokodaii str. 7	Mutation(s): 0  Gene Names: STK_15430, tmk 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	C [auth A], E [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
NI	D [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.259 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.934	α = 90
b = 63.222	β = 90
c = 138.565	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-12-30 
Deposition Author(s): Biswas, A., Jeyakanthan, J., Sekar, K.

Revision History  

• Version 1.0: 2015-12-30
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description