3N2I

2.25 Angstrom resolution crystal structure of a thymidylate kinase (tmk) from Vibrio cholerae O1 biovar eltor str. N16961 in complex with thymidine

• PDB DOI: https://doi.org/10.2210/pdb3N2I/pdb

• Classification: TRANSFERASE
• Organism(s): Vibrio cholerae O1 biovar El Tor str. N16961
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-05-18 Released: 2010-06-02 
• Deposition Author(s): Halavaty, A.S., Minasov, G., Shuvalova, L., Winsor, J., Dubrovska, I., Peterson, S., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.261 
• R-Value Work: 0.206 
• R-Value Observed: 0.208 

Starting Model: experimental

Literature

2.25 Angstrom resolution crystal structure of a thymidylate kinase (tmk) from Vibrio cholerae O1 biovar eltor str. N16961 in complex with thymidine

Halavaty, A.S., Minasov, G., Shuvalova, L., Winsor, J., Dubrovska, I., Peterson, S., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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: 53.43 kDa 
• Atom Count: 3,371 
• Modelled Residue Count: 415 
• Deposited Residue Count: 472 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidylate kinase	A, B	236	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 0  Gene Names: tmk, VC_2016 EC: 2.7.4.9
UniProt
Find proteins for Q9KQI2 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KQI2  Go to UniProtKB:  Q9KQI2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
THM	D [auth A], F [auth B]	THYMIDINE C10 H14 N2 O5 IQFYYKKMVGJFEH-XLPZGREQSA-N
CL	C [auth A], E [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.261 
• R-Value Work: 0.206 
• R-Value Observed: 0.208 
• Space Group: I 4₁ 2 2
• Diffraction Data: https://doi.org/10.18430/m33n2i

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.6	α = 90
b = 92.6	β = 90
c = 231.538	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-06-02 
Deposition Author(s): Halavaty, A.S., Minasov, G., Shuvalova, L., Winsor, J., Dubrovska, I., Peterson, S., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2010-06-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description