6M1C | pdb_00006m1c

Crystal structure of RsmD methyltransferase of M. tuberculosis in complex with sinefungin reveals key interactions

• PDB DOI: https://doi.org/10.2210/pdb6M1C/pdb

• Classification: TRANSFERASE
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-02-25 Released: 2021-06-02 
• Deposition Author(s): Bijpuria, S., Khan, S.H., Kumar, A., Taneja, B.
• Funding Organization(s): Department of Science & Technology (DST, India)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.236 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of RsmD methyltransferase of M. tuberculosis in complex with sinefungin reveals key interactions

Bijpuria, S., Khan, S.H., Kumar, A., Taneja, B.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 20.36 kDa 
• Atom Count: 1,463 
• Modeled Residue Count: 184 
• Deposited Residue Count: 189 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Possible methyltransferase (Methylase)	A	189	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: Rv2966c EC: 2.1.1 (UniProt), 2.1.1.171 (UniProt)
UniProt
Find proteins for I6XFS7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore I6XFS7  Go to UniProtKB:  I6XFS7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SFG (Subject of Investigation/LOI)	B [auth A]	SINEFUNGIN C15 H23 N7 O5 LMXOHSDXUQEUSF-YECHIGJVSA-N
ACT	C [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.236 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.191	α = 90
b = 55.191	β = 90
c = 99.641	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-06-02 
Deposition Author(s): Bijpuria, S., Khan, S.H., Kumar, A., Taneja, B.

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Funding Organization	Location	Grant Number
Department of Science & Technology (DST, India)	India	EMR/2016/003589

Revision History  

• Version 1.0: 2021-06-02
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Advisory, Data collection, Database references, Refinement description