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- EMDB-66709: Dimer of ATP-dependent diazotase Mco01_40450 -

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Basic information

Entry
Database: EMDB / ID: EMD-66709
TitleDimer of ATP-dependent diazotase Mco01_40450
Map data
Sample
  • Complex: Dimer of Mco01_40450
    • Other: ATP-dependent diazotase Mco01_40450
Keywordsdiazotase / enzyme / ATP-dependent / LIGASE
Function / homologymedium-chain fatty acid-CoA ligase activity / ANL, N-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily / fatty acid metabolic process / Fatty-acid-CoA ligase FadD
Function and homology information
Biological speciesMicrobispora corallina (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.08 Å
AuthorsNing J / Kawai S / Katsuyama Y / Ohnishi Y
Funding support Japan, 5 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)22H02192 Japan
Japan Society for the Promotion of Science (JSPS)25K01955 Japan
Japan Society for the Promotion of Science (JSPS)22H05130 Japan
Japan Society for the Promotion of Science (JSPS)19H05685 Japan
Japan Society for the Promotion of Science (JSPS)22KJ1046 Japan
CitationJournal: J.Am.Chem.Soc. / Year: 2026
Title: Promiscuous ATP-Dependent Diazotases Discovered by Comprehensive Genome Mining Based on Sequence Similarity Network Analysis
Authors: Ning J / Kawai S / Katsuyama Y / Ohnishi Y
History
DepositionOct 24, 2025-
Header (metadata) releaseAug 26, 2026-
Map releaseAug 26, 2026-
UpdateAug 26, 2026-
Current statusAug 26, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_66709.png

Downloads & links

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Map

FileDownload / File: emd_66709.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.75 Å/pix.
x 320 pix.
= 240. Å		0.75 Å/pix.
x 320 pix.
= 240. Å		0.75 Å/pix.
x 320 pix.
= 240. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.75 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.044768758 - 0.10367327
Average (Standard dev.)0.000018902283 (±0.002892707)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 240.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_66709_msk_1.map
Projections & Slices
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Half map: #1

Fileemd_66709_half_map_1.map
Projections & Slices
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Histogram

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Half map: #2

Fileemd_66709_half_map_2.map
Projections & Slices
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Sample components

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Entire : Dimer of Mco01_40450

EntireName: Dimer of Mco01_40450
Components
  • Complex: Dimer of Mco01_40450
    • Other: ATP-dependent diazotase Mco01_40450

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Supramolecule #1: Dimer of Mco01_40450

SupramoleculeName: Dimer of Mco01_40450 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Microbispora corallina (bacteria)
Molecular weightTheoretical: 63.2 KDa

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Macromolecule #1: ATP-dependent diazotase Mco01_40450

MacromoleculeName: ATP-dependent diazotase Mco01_40450 / type: other / ID: 1 / Classification: other
Source (natural)Organism: Microbispora corallina (bacteria)
SequenceString: MNHKVHHHHH HIEGRHMTLS HETVLTPEQR ARLAADPDLG GGNLLTKAIE ANPHPELPFI HLGRPLTVPS GEQRTELSLL DLDELVQSWS VWYLKQGVRP RDRVAIYLHD SFAYSVHFYA LAQIGAVAVL VNSKASRYIA TELCRQTNPV GVYTDLDHLE ILGEEFHLLP ...String:
MNHKVHHHHH HIEGRHMTLS HETVLTPEQR ARLAADPDLG GGNLLTKAIE ANPHPELPFI HLGRPLTVPS GEQRTELSLL DLDELVQSWS VWYLKQGVRP RDRVAIYLHD SFAYSVHFYA LAQIGAVAVL VNSKASRYIA TELCRQTNPV GVYTDLDHLE ILGEEFHLLP GLRWTQVAEE LPAPPPAKLP QEARFRHVDE DPVSILHSSG TTGRPKPVIQ THRSCVAGPR FRLVDHHEQP GAIMMTALPQ SHLGCIAYST YAVLGGTPLV PWYDTSGPEL AKAVEKYRPT TVMAFGHAYA ELAAADLPAG AIDSVNVWIS IGDAVHEKHI KTILGMRSAD RAPASFFDRL GTTELGWGVL LKVRTLADER NDRCVGKPVG VAEVAVLRRD GTEADVNEVG LLGAKGPAIT AGYWSDSDTT YRSKLSGFWL TGDMAYRDEA GNYFQVDRAV DAIETPTGTG YSVFMEELML NELPEVLDVA VVAGIHRGRT APVAVVTSSA ARPDAQKLLN EANEALRAAG HPELTMLEVA RSEEDFPVGV TGKVLKRRLR EKYSSLSTYI REGGGKSIGT ILNDVFV

UniProtKB: Fatty-acid-CoA ligase FadD
Recombinant expressionOrganism: Escherichia coli (E. coli)

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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

Concentration2.5 mg/mL
BufferpH: 7.2
Component:
ConcentrationFormulaName
200.0 mMNaClsodium chloride
20.0 mMNH2C(CH2OH)3ClTris chloride
1.0 mMNaNO2sodium nitrite
1.0 mMC10H16N5O13P3ATP
1.0 mMC9H11NO23-aminopheylproanoic acid
GridMaterial: COPPER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 273 K

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Electron microscopy

MicroscopeTFS TITAN THEMIS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 9276 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 812192
CTF correctionSoftware - Name: cryoSPARC (ver. 4.00) / Type: NONE
Startup modelType of model: INSILICO MODEL / In silico model: Model was build by AlphaFold2
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.08 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 237107
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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