3PZC

Crystal structure of class II aaRS homologue (Bll0957) complexed with Coenzyme A

• PDB DOI: https://doi.org/10.2210/pdb3PZC/pdb

• Classification: LIGASE
• Organism(s): Bradyrhizobium japonicum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-12-14 Released: 2011-10-19 
• Deposition Author(s): Weygand-Durasevic, I., Luic, M., Mocibob, M., Ivic, N., Subasic, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.223 
• R-Value Work: 0.167 
• R-Value Observed: 0.170 

Literature

Substrate Recognition by Novel Family of Amino Acid:[Carrier Protein] Ligases

Mocibob, M., Ivic, N., Subasic, D., Luic, M., Weygand-Durasevic, I.

(2011) Croat Chem Acta 84: 149-157

• DOI: https://doi.org/10.5562/cca1818

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 PISA (software)

Macromolecule Content

• Total Structure Weight: 77.98 kDa 
• Atom Count: 4,996 
• Modelled Residue Count: 572 
• Deposited Residue Count: 692 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Amino acid--[acyl-carrier-protein] ligase 1	A, B	346	Bradyrhizobium japonicum	Mutation(s): 0  Gene Names: bll0957 EC: 6.2.1
UniProt
Find proteins for Q89VT8 (Bradyrhizobium diazoefficiens (strain JCM 10833 / BCRC 13528 / IAM 13628 / NBRC 14792 / USDA 110)) Explore Q89VT8  Go to UniProtKB:  Q89VT8

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
COA	H [auth B]	COENZYME A C21 H36 N7 O16 P3 S RGJOEKWQDUBAIZ-IBOSZNHHSA-N
GAP	D [auth A]	GLYCYL-ADENOSINE-5'-PHOSPHATE C12 H17 N6 O8 P HROXHMRQKGGIFT-JJNLEZRASA-N
GOL	E [auth A], F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	C [auth A], G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT	I [auth B], J [auth B], K [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.223 
• R-Value Work: 0.167 
• R-Value Observed: 0.170 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.194	α = 90
b = 101.791	β = 90
c = 50.623	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
CrysalisPro	data collection
CrysalisPro	data reduction
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-10-19 
Deposition Author(s): Weygand-Durasevic, I., Luic, M., Mocibob, M., Ivic, N., Subasic, D.

Revision History  

• Version 1.0: 2011-10-19
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Refinement description
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references, Derived calculations