6K7S | pdb_00006k7s

Crystal structure of thymidylate synthase from shrimp

• PDB DOI: https://doi.org/10.2210/pdb6K7S/pdb

• Classification: TRANSFERASE
• Organism(s): Penaeus vannamei
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-06-08 Released: 2020-06-10 
• Deposition Author(s): Ma, Q., Zang, K., Liu, C.
• Funding Organization(s): Other government, Chinese Academy of Sciences, National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free: 
  0.198 (Depositor), 0.206 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.171 (DCC) 
• R-Value Observed: 
  0.162 (Depositor) 

Starting Model: experimental

Literature

Structural analysis of a shrimp thymidylate synthase reveals species-specific interactions with dUMP and raltitrexed.

Liu, C., Zang, K., Li, S., Li, F., Ma, Q.

(2020) J Oceanol Limnol 38: 1891-1899

• DOI: https://doi.org/10.1007/s00343-019-9184-8

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: 68.98 kDa 
• Atom Count: 5,185 
• Modeled Residue Count: 564 
• Deposited Residue Count: 584 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidylate synthase	A, B	292	Penaeus vannamei	Mutation(s): 0  Gene Names: TS EC: 2.1.1.45
UniProt
Find proteins for A0A423U5Z1 (Penaeus vannamei) Explore A0A423U5Z1  Go to UniProtKB:  A0A423U5Z1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
D16 (Subject of Investigation/LOI)	D [auth A], F [auth B]	TOMUDEX C21 H22 N4 O6 S IVTVGDXNLFLDRM-HNNXBMFYSA-N
UMP (Subject of Investigation/LOI)	C [auth A], E [auth B]	2'-DEOXYURIDINE 5'-MONOPHOSPHATE C9 H13 N2 O8 P JSRLJPSBLDHEIO-SHYZEUOFSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free:  0.198 (Depositor), 0.206 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.171 (DCC) 
• R-Value Observed: 0.162 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.653	α = 90
b = 83.674	β = 92.26
c = 55.157	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-06-10 
Deposition Author(s): Ma, Q., Zang, K., Liu, C.

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Funding Organization	Location	Grant Number
Other government	China	1000 talent program
Chinese Academy of Sciences	China	100 talent program
National Natural Science Foundation of China	China	--
National Natural Science Foundation of China	China	--

Revision History  

• Version 1.0: 2020-06-10
  Type: Initial release
  
• Version 1.1: 2021-06-30
  Changes: Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description