5G1F | pdb_00005g1f

Crystal structure of the 6-carboxyhexanoate-CoA ligase (BioW)from Bacillus subtilis in complex with coenzyme A

• PDB DOI: https://doi.org/10.2210/pdb5G1F/pdb

• Classification: LIGASE
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-03-25 Released: 2017-03-08 
• Deposition Author(s): Moynie, L., Wang, M., Campopiano, D.J., Naismith, J.H.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.252 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Starting Model: experimental

Literature

The Structure of the 6-Carboxyhexanoate-Coa Ligase from Bacillus Subtilis

Wang, M., Moynie, L., Campopiano, D.J., Naismith, J.H.

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 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 60.85 kDa 
• Atom Count: 4,060 
• Modeled Residue Count: 493 
• Deposited Residue Count: 520 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
6-CARBOXYHEXANOATE-COA LIGASE	A, B	260	Bacillus subtilis	Mutation(s): 0  EC: 6.2.1.14
UniProt
Find proteins for P53559 (Bacillus subtilis (strain 168)) Explore P53559  Go to UniProtKB:  P53559

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
COA	E [auth B]	COENZYME A C21 H36 N7 O16 P3 S RGJOEKWQDUBAIZ-IBOSZNHHSA-N
2PE	D [auth A]	NONAETHYLENE GLYCOL C18 H38 O10 YZUUTMGDONTGTN-UHFFFAOYSA-N
PML	C [auth A], F [auth B]	PIMELIC ACID C7 H12 O4 WLJVNTCWHIRURA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.252 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.59	α = 90
b = 78.36	β = 90
c = 166.43	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
XDS	data reduction
xia2	data scaling
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-03-08 
Deposition Author(s): Moynie, L., Wang, M., Campopiano, D.J., Naismith, J.H.

Revision History  

• Version 1.0: 2017-03-08
  Type: Initial release
  
• Version 2.0: 2017-06-21
  Changes: Advisory, Atomic model, Derived calculations
• Version 2.1: 2024-01-10
  Changes: Data collection, Database references, Other, Refinement description