8YND | pdb_00008ynd

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)

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
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history.

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

Macromolecule Content

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

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-grasp peptide ligase	A, B, C, D, E A, B, C, D, E, F, G, H	448	Streptomyces albogriseolus 1-36	Mutation(s): 0 Gene Names: Alb28
UniProt
Find proteins for A0ACD6BA05 (Streptomyces sp. SID14515) Explore A0ACD6BA05 Go to UniProtKB: A0ACD6BA05
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0ACD6BA05
Sequence Annotations Expand
Reference Sequence

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-02-19

Deposition Author(s):

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

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.