8YF3 | pdb_00008yf3

DNA cytosine C5-carboxymethyltransferase in complex with Cx-SAM

• PDB DOI: https://doi.org/10.2210/pdb8YF3/pdb

• Classification: TRANSFERASE
• Organism(s): Synechococcus phage S-B43
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-02-23 Released: 2025-09-03 
• Deposition Author(s): Yang, Q., Zhang, Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.264 (Depositor), 0.262 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.215 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

Starting Model: in silico

Literature

DNA cytosine-5-carboxymethyltransferase in complex with Cx-SAM

Yang, Q., Zhang, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 41.4 kDa 
• Atom Count: 2,778 
• Modeled Residue Count: 333 
• Deposited Residue Count: 372 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytosine-specific methyltransferase	A	372	Synechococcus phage S-B43	Mutation(s): 0  EC: 2.1.1.37
UniProt
Find proteins for A0A514ABG7 (Synechococcus phage S-B43) Explore A0A514ABG7  Go to UniProtKB:  A0A514ABG7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GEK (Subject of Investigation/LOI)	B [auth A]	(2S)-4-[{[(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}(carboxylatomethyl)sulfonio] -2-ammoniobutanoate C16 H22 N6 O7 S VFFTYSZNZJBRBG-HEOPWLPUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.264 (Depositor), 0.262 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.215 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.261	α = 90
b = 42.131	β = 96.05
c = 98.003	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-03 
Deposition Author(s): Yang, Q., Zhang, Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2025-09-03
  Type: Initial release