7S5M | pdb_00007s5m

Crystal Structure of a 8-amino-7-oxononanoate synthase/2-amino-3-ketobutyrate coenzyme A ligase from Mycobacterium smegmatis

• PDB DOI: https://doi.org/10.2210/pdb7S5M/pdb

• Classification: TRANSFERASE
• Organism(s): Mycolicibacterium smegmatis MC2 155
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-09-10 Released: 2021-09-22 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.274 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.230 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.232 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of a 8-amino-7-oxononanoate synthase/2-amino-3-ketobutyrate coenzyme A ligase from Mycobacterium smegmatis

Abendroth, J., Davies, D.R., Sankaran, B., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

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 Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 167.11 kDa 
• Atom Count: 10,728 
• Modeled Residue Count: 1,505 
• Deposited Residue Count: 1,616 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
8-amino-7-oxononanoate synthase	A, B, C, D	404	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0  Gene Names: bioF, MSMEG_3189, MSMEI_3107 EC: 2.3.1.47
UniProt
Find proteins for A0QX65 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QX65  Go to UniProtKB:  A0QX65

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.274 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.230 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.232 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m37s5m

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.71	α = 90
b = 108.94	β = 94.651
c = 108.34	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MoRDa	phasing
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-09-22 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2021-09-22
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description