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

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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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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

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 H [auth D] SDF format, chain I [auth E] SDF format, chain G [auth B] MOL2 format, chain H [auth D] MOL2 format, chain I [auth E] MOL2 format, chain G [auth B] mmCIF format, chain H [auth D] mmCIF format, chain I [auth E] mmCIF format, chain G [auth B]	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

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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

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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.