9LFY | pdb_00009lfy

Complex crystal structure of transaldolase AprG with GalNAc from Streptoalloteichus tenebrarius

PDB DOI: https://doi.org/10.2210/pdb9LFY/pdb

Classification: TRANSFERASE
Organism(s): Streptoalloteichus tenebrarius
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-01-09 Released: 2025-09-24
Deposition Author(s): Xie, Z.Z., Li, Q.R., Zhang, L.L., Huang, J.-W., He, Y.T., Chen, C.-C., Guo, R.-T.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.243 (Depositor), 0.243 (DCC)
R-Value Work:
0.206 (Depositor), 0.206 (DCC)
R-Value Observed:
0.208 (Depositor)

Starting Model: in silico
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Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Apramycin Biosynthesis: Structure and Mechanism of Action of a New-Type Transaldolase AprG from Streptoalloteichus tenebrarius

Xie, Z., Zhang, L., Li, Q., Huang, J.W., He, Y., Zhang, H., Wang, X., Min, J., Chen, C.C., Guo, R.T.

(2025) ACS Catal : 16186-16196

DOI: https://doi.org/10.1021/acscatal.5c02753

Macromolecule Content

Total Structure Weight: 226.5 kDa
Atom Count: 16,232
Modeled Residue Count: 2,011
Deposited Residue Count: 2,070
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AprG	A, B, C, D, E A, B, C, D, E, F	345	Streptoalloteichus tenebrarius	Mutation(s): 0 Gene Names: aprG
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG (Subject of Investigation/LOI) Query on PEG Download Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain H [auth D] SDF format, chain I [auth E] MOL2 format, chain G [auth B] MOL2 format, chain H [auth D] MOL2 format, chain I [auth E] mmCIF format, chain G [auth B] mmCIF format, chain H [auth D] mmCIF format, chain I [auth E]	G [auth B], H [auth D], I [auth E]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Focus chain H [auth D] Focus chain I [auth E] Interactions & Density Focus chain G [auth B] Focus chain H [auth D] Focus chain I [auth E]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
A1EJZ Query on A1EJZ	A, B, C, D, E A, B, C, D, E, F	L-PEPTIDE LINKING	C₁₄ H₂₇ N₃ O₇		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.243 (Depositor), 0.243 (DCC)
R-Value Work: 0.206 (Depositor), 0.206 (DCC)
R-Value Observed: 0.208 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.889	α = 90
b = 141.231	β = 101.49
c = 129.333	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SAINT	data scaling
SAINT	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-09-24

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2025-09-24
Type: Initial release

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.