6AC6

Ab initio crystal structure of Selenomethionine labelled Mycobacterium smegmatis Mfd

• PDB DOI: https://doi.org/10.2210/pdb6AC6/pdb

• Classification: HYDROLASE
• Organism(s): Mycolicibacterium smegmatis MC2 155
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-07-25 Released: 2019-08-28 
• Deposition Author(s): Putta, S., Fox, G.C., Walsh, M.A., Rao, D.N., Nagaraja, V., Natesh, R.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.99 Å
• R-Value Free: 0.270 
• R-Value Work: 0.218 
• R-Value Observed: 0.221 

Literature

Structural basis for nucleotide-mediated remodelling mechanism of Mycobacterium Mfd

Putta, S., Prabha, S., Bhat, V., Fox, G.C., Walsh, M.A., Rao, D.N., Nagaraja, V., Natesh, R.

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.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 269.89 kDa 
• Atom Count: 16,853 
• Modelled Residue Count: 2,307 
• Deposited Residue Count: 2,470 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mycobacterium smegmatis Mfd	A, B	1,235	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0  Gene Names: mfd EC: 3.6.4
UniProt
Find proteins for A0R3C5 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0R3C5  Go to UniProtKB:  A0R3C5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth A], F [auth B], G [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.99 Å
• R-Value Free: 0.270 
• R-Value Work: 0.218 
• R-Value Observed: 0.221 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.71	α = 90
b = 158.87	β = 90
c = 207.94	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
CRANK2	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-08-28 
Deposition Author(s): Putta, S., Fox, G.C., Walsh, M.A., Rao, D.N., Nagaraja, V., Natesh, R.

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Funding Organization	Location	Grant Number
Other government	India	BT/HRD/35/02/19/2009

Revision History  

• Version 1.0: 2019-08-28
  Type: Initial release