9W3P | pdb_00009w3p

YcfA from Erwinia amylovora

PDB DOI: https://doi.org/10.2210/pdb9W3P/pdb
EM Map EMD-64007: EMDB EMDataResource

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Erwinia amylovora ATCC 49946
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-07-29 Released: 2026-08-05
Deposition Author(s): Zhang, L., Dou, C., Jia, X.Y., Zhu, X.F., Cheng, W.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.44 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9W3P

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

Literature

Mechanistic Insights into Thioamide Formation by The YcfA-YcfC Enzyme System in 6-Thioguanine Biosynthesis

Zhang, L.

To be published.

Macromolecule Content

Total Structure Weight: 365.93 kDa
Atom Count: 24,126
Modeled Residue Count: 3,065
Deposited Residue Count: 3,276
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Asparagine synthetase domain-containing protein	A [auth B] B [auth D] C [auth G] D [auth I] E [auth J] A [auth B], B [auth D], C [auth G], D [auth I], E [auth J], F [auth K], G [auth M], H [auth A], I [auth C], J [auth E], K [auth F], L [auth H], M [auth L], N	234	Erwinia amylovora ATCC 49946	Mutation(s): 0 Gene Names: BN437_1047
UniProt
Find proteins for A0A831ERP2 (Erwinia amylovora NBRC 12687 = CFBP 1232) Explore A0A831ERP2 Go to UniProtKB: A0A831ERP2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A831ERP2
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.44 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-08-05

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32200114

Revision History (Full details and data files)

Version 1.0: 2026-08-05
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.