8K1F

Crystal Structure of TrmR from Fusobacterium nucleatum

• PDB DOI: https://doi.org/10.2210/pdb8K1F/pdb

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


• Deposited: 2023-07-10 Released: 2023-08-02 
• 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: 2.40 Å
• R-Value Free: 0.292 
• R-Value Work: 0.213 
• R-Value Observed: 0.221 

Literature

Crystal Structure of TrmR 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)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 75.21 kDa 
• Atom Count: 4,374 
• Modelled Residue Count: 572 
• Deposited Residue Count: 645 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA 5-hydroxyuridine methyltransferase	A, B, C	215	Fusobacterium nucleatum subsp. nucleatum ATCC 25586	Mutation(s): 0  Gene Names: trmR, FN0314 EC: 2.1.1
UniProt
Find proteins for Q8RGI1 (Fusobacterium nucleatum subsp. nucleatum (strain ATCC 25586 / DSM 15643 / BCRC 10681 / CIP 101130 / JCM 8532 / KCTC 2640 / LMG 13131 / VPI 4355)) Explore Q8RGI1  Go to UniProtKB:  Q8RGI1

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.292 
• R-Value Work: 0.213 
• R-Value Observed: 0.221 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 165.281	α = 90
b = 46.589	β = 98.33
c = 87.316	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-08-02 
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: 2023-08-02
  Type: Initial release