7E3S | pdb_00007e3s

Crystal structure of TrmL from Shewanella oneidensis

• PDB DOI: https://doi.org/10.2210/pdb7E3S/pdb

• Classification: TRANSFERASE
• Organism(s): Shewanella oneidensis MR-1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-02-09 Released: 2022-02-16 
• Deposition Author(s): Kim, J., Son, J.
• Funding Organization(s): National Research Foundation (NRF, Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.239 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of TrmL from Shewanella oneidensis

Kim, J., Son, J.

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 Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 40.77 kDa 
• Atom Count: 2,341 
• Modeled Residue Count: 300 
• Deposited Residue Count: 368 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA (cytidine(34)-2'-O)-methyltransferase	A, B	184	Shewanella oneidensis MR-1	Mutation(s): 0  Gene Names: trmL, SO_4529 EC: 2.1.1.207
UniProt
Find proteins for Q8E8X2 (Shewanella oneidensis (strain ATCC 700550 / JCM 31522 / CIP 106686 / LMG 19005 / NCIMB 14063 / MR-1)) Explore Q8E8X2  Go to UniProtKB:  Q8E8X2

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.239 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.816	α = 90
b = 77.988	β = 90
c = 101.044	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-02-16 
Deposition Author(s): Kim, J., Son, J.

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

Revision History  

• Version 1.0: 2022-02-16
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description