8K5L | pdb_00008k5l

Structure of tRNA (cmo5U34)-methyltransferase from Fusobacterium nucleatum

• PDB DOI: https://doi.org/10.2210/pdb8K5L/pdb

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


• Deposited: 2023-07-22 Released: 2023-08-23 
• Deposition Author(s): He, S.R., Bai, X.
• Funding Organization(s): National Research Foundation (NRF, Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.67 Å
• R-Value Free: 
  0.257 (Depositor), 0.257 (DCC) 
• R-Value Work: 
  0.225 (Depositor), 0.226 (DCC) 
• R-Value Observed: 
  0.227 (Depositor) 

Starting Model: in silico

Literature

Crystal Structure of CmoA 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)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 198.04 kDa 
• Atom Count: 13,108 
• Modeled Residue Count: 1,596 
• Deposited Residue Count: 1,688 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA (cmo5U34)-methyltransferase	A, B, C, D, E, F, G, H	211	Fusobacterium nucleatum	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.67 Å
• R-Value Free:  0.257 (Depositor), 0.257 (DCC) 
• R-Value Work:  0.225 (Depositor), 0.226 (DCC) 
• R-Value Observed: 0.227 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.955	α = 90.03
b = 58.98	β = 90.03
c = 139.69	γ = 90.05

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: 2023-08-23 
Deposition Author(s): He, S.R., Bai, X.

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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