8K76 | pdb_00008k76

Crystal structure of S-adenosylmethionine-dependent methyltransferase from Fusobacterium nucleatum

• PDB DOI: https://doi.org/10.2210/pdb8K76/pdb

• Classification: TRANSFERASE
• Organism(s): Fusobacterium nucleatum subsp. nucleatum ATCC 25586
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2023-07-26 Released: 2023-08-23 
• Deposition Author(s): He, S.R., Bai, X., Zhang, J., Zhao, Z.D.
• Funding Organization(s): National Research Foundation (NRF, Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.49 Å
• R-Value Free: 
  0.227 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.215 (Depositor) 

Literature

Crystal structure of S-adenosylmethionine-dependent methyltransferase from Fusobacterium nucleatum

He, S.R., Bai, X.

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: 57.23 kDa 
• Atom Count: 3,821 
• Modeled Residue Count: 478 
• Deposited Residue Count: 498 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
S-adenosylmethionine-dependent methyltransferase	A, B	249	Fusobacterium nucleatum subsp. nucleatum ATCC 25586	Mutation(s): 0  Gene Names: FN1919 EC: 2.1.1
UniProt
Find proteins for Q8R6D8 (Fusobacterium nucleatum subsp. nucleatum (strain ATCC 25586 / DSM 15643 / BCRC 10681 / CIP 101130 / JCM 8532 / KCTC 2640 / LMG 13131 / VPI 4355)) Explore Q8R6D8  Go to UniProtKB:  Q8R6D8

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.49 Å
• R-Value Free:  0.227 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.215 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.981	α = 90
b = 80.629	β = 90
c = 108.49	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-08-23 
Deposition Author(s): He, S.R., Bai, X., Zhang, J., Zhao, Z.D.

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Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	--

Revision History  

• Version 1.0: 2023-08-23
  Type: Initial release