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- EMDB-60345: The cryoEM structure of a daminobutyrate--2-oxoglutarate transami... -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-60345
TitleThe cryoEM structure of a daminobutyrate--2-oxoglutarate transaminase EctB
Map data
Sample
  • Complex: Cyclodipeptide oxidase Complex
    • Protein or peptide: Diaminobutyrate-2-oxoglutarate transaminase
  • Ligand: PYRIDOXAL-5'-PHOSPHATE
Keywordsdaminobutyrate--2-oxoglutarate transaminase / TRANSFERASE
Function / homology
Function and homology information


diaminobutyrate-2-oxoglutarate transaminase / diaminobutyrate-2-oxoglutarate transaminase activity / aromatic-L-amino-acid decarboxylase activity / carboxylic acid metabolic process / pyridoxal phosphate binding / cytoplasm
Similarity search - Function
Pyridoxal phosphate-dependent decarboxylase / Pyridoxal-dependent decarboxylase conserved domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Diaminobutyrate-2-oxoglutarate transaminase
Similarity search - Component
Biological speciesActinomadura oligospora ATCC 43269 (bacteria) / Parageobacillus caldoxylosilyticus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.12 Å
AuthorsJiang WX / Cheng XQ / Ma LX / Xing Q
Funding support China, 1 items
OrganizationGrant numberCountry
National Basic Research Program of China (973 Program)2021YFC2100100 China
CitationJournal: To Be Published
Title: The cryoEM structure of a daminobutyrate--2-oxoglutarate transaminase EctB
Authors: Jiang WX / Cheng XQ / Ma LX / Xing Q
History
DepositionMay 30, 2024-
Header (metadata) releaseJun 4, 2025-
Map releaseJun 4, 2025-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60345.png

Downloads & links

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Map

FileDownload / File: emd_60345.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.57 Å/pix.
x 400 pix.
= 226.666 Å		0.57 Å/pix.
x 400 pix.
= 226.666 Å		0.57 Å/pix.
x 400 pix.
= 226.666 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.56667 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.057
Minimum - Maximum-0.41179812 - 0.673796
Average (Standard dev.)0.00015733071 (±0.016280297)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 226.6664 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_60345_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_60345_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 : Cyclodipeptide oxidase Complex

EntireName: Cyclodipeptide oxidase Complex
Components
  • Complex: Cyclodipeptide oxidase Complex
    • Protein or peptide: Diaminobutyrate-2-oxoglutarate transaminase
  • Ligand: PYRIDOXAL-5'-PHOSPHATE

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Supramolecule #1: Cyclodipeptide oxidase Complex

SupramoleculeName: Cyclodipeptide oxidase Complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Actinomadura oligospora ATCC 43269 (bacteria)

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Macromolecule #1: Diaminobutyrate-2-oxoglutarate transaminase

MacromoleculeName: Diaminobutyrate-2-oxoglutarate transaminase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: diaminobutyrate-2-oxoglutarate transaminase
Source (natural)Organism: Parageobacillus caldoxylosilyticus (bacteria)
Molecular weightTheoretical: 54.218809 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MNLDFLPNDA FIEPSGQNIN EVASLIKKFM DLVIENSASS EQRPPLSQIE NYTFGEFPVQ GIPTEGILLQ LKEILRNSMN PLTPNYIGH MDSIPTLISC LGEFVTTTLN NNMLSLEMSP VFSQMEVQVL RKIARMFGYD EQSGGVMVSG GSLANLQALA V ARNHYFSV ...String:
MNLDFLPNDA FIEPSGQNIN EVASLIKKFM DLVIENSASS EQRPPLSQIE NYTFGEFPVQ GIPTEGILLQ LKEILRNSMN PLTPNYIGH MDSIPTLISC LGEFVTTTLN NNMLSLEMSP VFSQMEVQVL RKIARMFGYD EQSGGVMVSG GSLANLQALA V ARNHYFSV KEDGLTGLIE QPVILASEAS HTSLHKAAML LGLGTSSVVA VKTNQNSQMD TSDLEKKINK TIEEGKQPFA VV ATAGTTV TGNIDPILSI AEITKKYGLW LHVDAAYGGA LVFSDKHRER LSGIEKADSI TFNPQKWMYV AKTCAMVLFK NRD LLETEF RISAPYMNDT DFTNLGEISV QGTRHADILK LYLSLQHIGL KSYDQLINEG YLRVEEFVKQ VKQRPYLELA SEPD TNICC FRGRPKNLDE KQCDQWNLEL QQFLLHKERV FFSLPTYRGK RWLRAVLLNP FTPISTIQKI FKTIDEFYIN HHSYN S

UniProtKB: Diaminobutyrate-2-oxoglutarate transaminase

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Macromolecule #2: PYRIDOXAL-5'-PHOSPHATE

MacromoleculeName: PYRIDOXAL-5'-PHOSPHATE / type: ligand / ID: 2 / Number of copies: 2 / Formula: PLP
Molecular weightTheoretical: 247.142 Da
Chemical component information

ChemComp-PLP:
PYRIDOXAL-5'-PHOSPHATE

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 35.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: OTHER / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 50339
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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