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- PDB-9w3p: YcfA from Erwinia amylovora -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 9w3p
TitleYcfA from Erwinia amylovora
ComponentsAsparagine synthetase domain-containing protein
KeywordsBIOSYNTHETIC PROTEIN / adenylation activity / L-Cys addition / YcfA-YcfC bipartite enzyme system / tetradecamer / 6-Thioguanine biosynthesis
Function / homologyRossmann-like alpha/beta/alpha sandwich fold / Asparagine synthetase domain-containing protein
Function and homology information
Biological speciesErwinia amylovora ATCC 49946 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.44 Å
AuthorsZhang, L. / Dou, C. / Jia, X.Y. / Zhu, X.F. / Cheng, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32200114 China
CitationJournal: To Be Published
Title: Mechanistic Insights into Thioamide Formation by The YcfA-YcfC Enzyme System in 6-Thioguanine Biosynthesis
Authors: Zhang, L.
History
DepositionJul 29, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 5, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Asparagine synthetase domain-containing protein
D: Asparagine synthetase domain-containing protein
G: Asparagine synthetase domain-containing protein
I: Asparagine synthetase domain-containing protein
J: Asparagine synthetase domain-containing protein
K: Asparagine synthetase domain-containing protein
M: Asparagine synthetase domain-containing protein
A: Asparagine synthetase domain-containing protein
C: Asparagine synthetase domain-containing protein
E: Asparagine synthetase domain-containing protein
F: Asparagine synthetase domain-containing protein
H: Asparagine synthetase domain-containing protein
L: Asparagine synthetase domain-containing protein
N: Asparagine synthetase domain-containing protein


Theoretical massNumber of molelcules
Total (without water)365,93114
Polymers365,93114
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Asparagine synthetase domain-containing protein


Mass: 26137.902 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Details: Sequence reference for Erwinia amylovora (strain ATCC 49946) (716540) is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt ID A0A831ERP2.
Source: (gene. exp.) Erwinia amylovora ATCC 49946 (bacteria)
Gene: BN437_1047 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A831ERP2
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: YcfA from Erwinia amylovora / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.36 MDa / Experimental value: NO
Source (natural)Organism: Erwinia amylovora ATCC 49946 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: NITROGEN

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 1100 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

EM software
IDNameCategory
1EMAN2particle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.44 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 16706 / Symmetry type: POINT

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