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- EMDB-64007: YcfA from Erwinia amylovora -

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Basic information

Entry
Database: EMDB / ID: EMD-64007
TitleYcfA from Erwinia amylovora
Map data
Sample
  • Complex: YcfA from Erwinia amylovora
    • Protein or peptide: Asparagine synthetase domain-containing protein
Keywordsadenylation activity / L-Cys addition / YcfA-YcfC bipartite enzyme system / tetradecamer / 6-Thioguanine biosynthesis / BIOSYNTHETIC PROTEIN
Biological speciesErwinia amylovora ATCC 49946 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.44 Å
AuthorsZhang L / Dou C / Jia XY / Zhu XF / Cheng W
Funding support China, 1 items
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
DepositionApr 3, 2025-
Header (metadata) releaseApr 8, 2026-
Map releaseApr 8, 2026-
UpdateApr 8, 2026-
Current statusApr 8, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64007.png

Downloads & links

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Map

FileDownload / File: emd_64007.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 256 pix.
= 217.6 Å		0.85 Å/pix.
x 256 pix.
= 217.6 Å		0.85 Å/pix.
x 256 pix.
= 217.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.133
Minimum - Maximum-0.14987925 - 0.36564127
Average (Standard dev.)0.004716379 (±0.025215067)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 217.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_64007_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_64007_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : YcfA from Erwinia amylovora

EntireName: YcfA from Erwinia amylovora
Components
  • Complex: YcfA from Erwinia amylovora
    • Protein or peptide: Asparagine synthetase domain-containing protein

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Supramolecule #1: YcfA from Erwinia amylovora

SupramoleculeName: YcfA from Erwinia amylovora / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Erwinia amylovora ATCC 49946 (bacteria)
Molecular weightTheoretical: 360 KDa

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Macromolecule #1: Asparagine synthetase domain-containing protein

MacromoleculeName: Asparagine synthetase domain-containing protein / type: protein_or_peptide / ID: 1
Details: The sequence of organism Erwinia amylovora ATCC 49946 is not available during the biocuration, replaced by A0A831ERP2 temporarily.
Enantiomer: LEVO
Source (natural)Organism: Erwinia amylovora ATCC 49946 (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTNQYSVKPQ LVMFTGGRDS TLAACYLMLQ GIPVHLWSGN SGCSLHRGIL SHRVEEMKNR FGDLVVGHTV ADISGAFRSI AIEALEQDI LKYRKNLVLL GEKLAIHAHL VDFCRRNDIN TINDGITHYQ MEFPEQRLVA KTFLMEMMAQ YDINYQSPVY E FAQSADDV ...String:
MTNQYSVKPQ LVMFTGGRDS TLAACYLMLQ GIPVHLWSGN SGCSLHRGIL SHRVEEMKNR FGDLVVGHTV ADISGAFRSI AIEALEQDI LKYRKNLVLL GEKLAIHAHL VDFCRRNDIN TINDGITHYQ MEFPEQRLVA KTFLMEMMAQ YDINYQSPVY E FAQSADDV KYRLLQLGIS TKSLEGISIF ADSFSTPSDD VVLAYLREKA PLAHNIVNFL AGETLNPPVL NNSAAA

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statecell

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: NITROGEN

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 49.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.44 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 16078
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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