8YND

ATP-grasp peptide ligase from Streptomyces

• PDB DOI: https://doi.org/10.2210/pdb8YND/pdb

• Classification: LIGASE
• Organism(s): Streptomyces albogriseolus 1-36
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-03-11 Released: 2025-02-19 
• Deposition Author(s): Xu, M.J., Yan, Y.Q.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free: 
  0.263 (Depositor), 0.262 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.213 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Starting Model: in silico

Literature

Structural Insights into the Substrate Recognition Mechanism of an ATP-Grasp Peptide-Ligase Producing Diverse Dipeptides Containing Unnatural Amino Acids

Yan, Y.Q., Li, S.Y., Wu, X.N., Zhou, T., Li, J.X., Huang, S.X., Zheng, J.T., Xu, J., Da, L.T., Xu, M.J.

(2025) ACS Catal 15: 2550-2560

• DOI: https://doi.org/10.1021/acscatal.4c07750

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.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 393.55 kDa 
• Atom Count: 27,004 
• Modelled Residue Count: 3,308 
• Deposited Residue Count: 3,584 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-grasp peptide ligase	A, B, C, D, E, F, G, H	448	Streptomyces albogriseolus 1-36	Mutation(s): 0  Gene Names: Alb28

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free:  0.263 (Depositor), 0.262 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.213 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.928	α = 99.54
b = 100.641	β = 101.88
c = 131.555	γ = 115.94

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-02-19 
Deposition Author(s): Xu, M.J., Yan, Y.Q.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	22177072

Revision History  

• Version 1.0: 2025-02-19
  Type: Initial release
  
• Version 1.1: 2025-02-26
  Changes: Database references