4WD3

Crystal structure of an L-amino acid ligase RizA

• PDB DOI: https://doi.org/10.2210/pdb4WD3/pdb

• Classification: LIGASE
• Organism(s): Bacillus subtilis subsp. subtilis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2014-09-06 Released: 2015-09-09 
• Deposition Author(s): Kagawa, W., Arai, T., Kino, K., Kurumizaka, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.255 
• R-Value Work: 0.201 
• R-Value Observed: 0.204 

Literature

Structure of RizA, an L-amino-acid ligase from Bacillus subtilis.

Kagawa, W., Arai, T., Ishikura, S., Kino, K., Kurumizaka, H.

(2015) Acta Crystallogr F Struct Biol Commun 71: 1125-1130

• PubMed: 26323296 
• DOI: https://doi.org/10.1107/S2053230X15012698
• Primary Citation of Related Structures:  
  4WD3


• PubMed Abstract: 
  

  RizA is an L-amino-acid ligase from Bacillus subtilis that participates in the biosynthesis of rhizocticin, an oligopeptide antibiotic. The substrate-free form of RizA has been crystallized and the structure was solved at 2.8 Å resolution. The amino-acid-binding site appears to be capable of accommodating multiple amino acids, consistent with previous biochemical studies.

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Organizational Affiliation: 

Department of Interdisciplinary Science and Engineering, Program in Chemistry and Life Science, School of Science and Engineering, Meisei University, 2-1-1 Hodokubo, Hino-shi, Tokyo 191-8506, Japan.

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: 93.91 kDa 
• Atom Count: 6,114 
• Modelled Residue Count: 776 
• Deposited Residue Count: 826 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-amino acid ligase	A, B	413	Bacillus subtilis subsp. subtilis	Mutation(s): 2  Gene Names: rizA
UniProt
Find proteins for B5UAT8 (Bacillus subtilis) Explore B5UAT8  Go to UniProtKB:  B5UAT8

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.255 
• R-Value Work: 0.201 
• R-Value Observed: 0.204 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.38	α = 90
b = 87.29	β = 97.52
c = 85.26	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-09-09 
Deposition Author(s): Kagawa, W., Arai, T., Kino, K., Kurumizaka, H.

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Funding Organization	Location	Grant Number
	Japan	--

Revision History  

• Version 1.0: 2015-09-09
  Type: Initial release
  
• Version 1.1: 2020-01-01
  Changes: Data collection, Database references, Derived calculations