8RI0

Crystal structure of Tm1570 domain from Calditerrivibrio nitroreducens in complex with S-adenosyl-L-methionine

• PDB DOI: https://doi.org/10.2210/pdb8RI0/pdb

• Classification: TRANSFERASE
• Organism(s): Calditerrivibrio nitroreducens DSM 19672
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-12-18 Released: 2024-01-10 
• Deposition Author(s): Kluza, A., Lewandowska, I., Sulkowska, J.
• Funding Organization(s): Polish National Science Centre, European Union (EU)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.250 
• R-Value Work: 0.206 
• R-Value Observed: 0.209 

Literature

Are there double knots in proteins? Prediction and in vitro verification based on TrmD-Tm1570 fusion from C. nitroreducens. To be published

Sulkowska, 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: 47.73 kDa 
• Atom Count: 2,727 
• Modelled Residue Count: 340 
• Deposited Residue Count: 410 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA (guanine-N(1)-)-methyltransferase	A, B	205	Calditerrivibrio nitroreducens DSM 19672	Mutation(s): 0  Gene Names: trmD, Calni_2012 EC: 2.1.1.228
UniProt
Find proteins for E4THH1 (Calditerrivibrio nitroreducens (strain DSM 19672 / NBRC 101217 / Yu37-1)) Explore E4THH1  Go to UniProtKB:  E4THH1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM (Subject of Investigation/LOI)	C [auth A], D [auth B]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.250 
• R-Value Work: 0.206 
• R-Value Observed: 0.209 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.85	α = 90
b = 48.09	β = 116.22
c = 79.81	γ = 90

Software Package:

Software Name	Purpose
MxCuBE	data collection
XDS	data reduction
XDS	data scaling
PHASER	phasing
PHENIX	refinement
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-01-10 
Deposition Author(s): Kluza, A., Lewandowska, I., Sulkowska, J.

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Funding Organization	Location	Grant Number
Polish National Science Centre	Poland	2018/31/B/NZ1/04016
European Union (EU)	European Union	COST EUTOPIA action

Revision History  

• Version 1.0: 2024-01-10
  Type: Initial release