9O57 | pdb_00009o57

Crystal structure of Thymidylate kinase (Tmk) from Klebsiella aerogenes.

• PDB DOI: https://doi.org/10.2210/pdb9O57/pdb

• Classification: TRANSFERASE
• Organism(s): Klebsiella aerogenes KCTC 2190
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-04-09 Released: 2025-04-16 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/Office of the Director

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 
  0.268 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.238 (Depositor), 0.244 (DCC) 
• R-Value Observed: 
  0.240 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Thymidylate kinase (Tmk) from Klebsiella aerogenes.

Liu, L., Lovell, S., Seibold, S., Battaile, K.P.

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 Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 49.75 kDa 
• Atom Count: 2,893 
• Modeled Residue Count: 370 
• Deposited Residue Count: 442 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidylate kinase	A, B	221	Klebsiella aerogenes KCTC 2190	Mutation(s): 0  Gene Names: tmk, CWM85_24435, N5C89_07930, NP224_17505 EC: 2.7.4.9
UniProt
Find proteins for A0A0J2I384 (Klebsiella michiganensis) Explore A0A0J2I384  Go to UniProtKB:  A0A0J2I384

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	C [auth A], D [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free:  0.268 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.238 (Depositor), 0.244 (DCC) 
• R-Value Observed: 0.240 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M39O57

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.407	α = 90
b = 75.45	β = 90
c = 76.018	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-04-16 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease, Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	75N93022C00036
National Institutes of Health/Office of the Director	United States	S10OD030394

Revision History  

• Version 1.0: 2025-04-16
  Type: Initial release