4S17 | pdb_00004s17

The crystal structure of glutamine synthetase from Bifidobacterium adolescentis ATCC 15703

• PDB DOI: https://doi.org/10.2210/pdb4S17/pdb

• Classification: LIGASE
• Organism(s): Bifidobacterium adolescentis ATCC 15703
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-01-08 Released: 2015-01-28 
• Deposition Author(s): Cuff, M., Tan, K., Mack, J., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.287 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.238 (Depositor), 0.242 (DCC) 
• R-Value Observed: 
  0.241 (Depositor) 

Literature

The crystal structure of glutamine synthetase from Bifidobacterium adolescentis ATCC 15703

Cuff, M., Tan, K., Mack, J., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D6  (Explore in 3D)
Global Stoichiometry: Homo 12-mer - A12 

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

Macromolecule Content 

• Total Structure Weight: 322.96 kDa 
• Atom Count: 21,259 
• Modeled Residue Count: 2,699 
• Deposited Residue Count: 2,886 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamine synthetase	A, B, C, D, E, F	481	Bifidobacterium adolescentis ATCC 15703	Mutation(s): 0  Gene Names: BAD_0943, glnA1 EC: 6.3.1.2
UniProt
Find proteins for A1A1Z1 (Bifidobacterium adolescentis (strain ATCC 15703 / DSM 20083 / NCTC 11814 / E194a)) Explore A1A1Z1  Go to UniProtKB:  A1A1Z1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	H [auth B], J [auth C]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
MG	G [auth A], I [auth B], K [auth C], L [auth D], M [auth E], N [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.287 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.238 (Depositor), 0.242 (DCC) 
• R-Value Observed: 0.241 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 134.052	α = 90
b = 134.052	β = 90
c = 298.915	γ = 120

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
DM	model building
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-01-28 
Deposition Author(s): Cuff, M., Tan, K., Mack, J., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2015-01-28
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary