7ED1 | pdb_00007ed1

Transferase from Mycobacterium smegmatis

• PDB DOI: https://doi.org/10.2210/pdb7ED1/pdb

• Classification: TRANSFERASE
• Organism(s): Mycolicibacterium smegmatis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-03-15 Released: 2022-03-16 
• Deposition Author(s): Kim, D.-G., Lee, B.-J., Lee, S.J.
• Funding Organization(s): National Research Foundation (NRF, Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.215 (Depositor), 0.201 (DCC) 
• R-Value Work: 
  0.182 (Depositor) 
• R-Value Observed: 
  0.184 (Depositor) 

Literature

Transferase from Mycobacterium smegmatis

Kim, D.-G., Lee, B.-J., Lee, S.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 (software)

Macromolecule Content 

• Total Structure Weight: 50.61 kDa 
• Atom Count: 3,928 
• Modeled Residue Count: 446 
• Deposited Residue Count: 446 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4'-phosphopantetheinyl transferase	A, B	223	Mycolicibacterium smegmatis	Mutation(s): 0  Gene Names: ERS451418_02655
UniProt
Find proteins for A0QVP7 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QVP7  Go to UniProtKB:  A0QVP7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
COA (Subject of Investigation/LOI)	C [auth A], H [auth B]	COENZYME A C21 H36 N7 O16 P3 S RGJOEKWQDUBAIZ-IBOSZNHHSA-N
1PE (Subject of Investigation/LOI)	D [auth A], I [auth B]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)	E [auth A], F [auth A], G [auth A], J [auth B], K [auth B], L [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.215 (Depositor), 0.201 (DCC) 
• R-Value Work:  0.182 (Depositor) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.559	α = 90
b = 73.858	β = 94.73
c = 65.196	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-03-16 
Deposition Author(s): Kim, D.-G., Lee, B.-J., Lee, S.J.

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Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	NRF-2018R1A2A1A19018526
National Research Foundation (NRF, Korea)	Korea, Republic Of	NRF-2018R1A5A2024425
National Research Foundation (NRF, Korea)	Korea, Republic Of	2020R1F1A1075828

Revision History  

• Version 1.0: 2022-03-16
  Type: Initial release
  
• Version 1.1: 2024-05-29
  Changes: Data collection
• Version 2.0: 2024-08-14
  Type: Coordinate replacement
  Reason: Ligand identity
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Refinement description, Source and taxonomy, Structure summary