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- PDB-9xbs: ATP-dependent diazotase Mco01_40450 binding with substrate -

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Basic information

Entry
Database: PDB / ID: 9xbs
TitleATP-dependent diazotase Mco01_40450 binding with substrate
ComponentsFatty-acid-CoA ligase FadD
KeywordsLIGASE / diazotase / enzyme / ATP-dependent
Function / homology
Function and homology information


medium-chain fatty acid-CoA ligase activity / fatty acid metabolic process
Similarity search - Function
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
Similarity search - Domain/homology
4-AMINOHYDROCINNAMIC ACID / ADENOSINE MONOPHOSPHATE / DIPHOSPHATE / Fatty-acid-CoA ligase FadD
Similarity search - Component
Biological speciesMicrobispora corallina (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.16 Å
AuthorsNing, J. / Kawai, S. / Katsuyama, Y. / Ohnishi, Y.
Funding support Japan, 5items
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, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 26, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 26, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Aug 26, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 26, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 26, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 26, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Aug 26, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Fatty-acid-CoA ligase FadD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,9534
Polymers63,2671
Non-polymers6863
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 Fatty-acid-CoA ligase FadD / ATP-dependent diazotase Mco01_40450


Mass: 63266.629 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Microbispora corallina (bacteria) / Gene: Mco01_40450 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0ABQ4G1Y4
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#3: Chemical ChemComp-DPO / DIPHOSPHATE


Mass: 173.943 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O7P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-AHC / 4-AMINOHYDROCINNAMIC ACID


Mass: 165.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11NO2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: Monomer of Mco01_40450 binding with substrates / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.0632 MDa / Experimental value: YES
Source (natural)Organism: Microbispora corallina (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.2
Buffer component
IDConc.NameFormulaBuffer-ID
1200 mMsodium chlorideNaCl1
220 mMTris chlorideNH2C(CH2OH)3Cl1
31 mMsodium nitriteNaNO21
41 mMATPC10H16N5O13P31
51 mM3-aminopheylproanoic acidC9H11NO21
SpecimenConc.: 2.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 291 K

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Electron microscopy imaging

MicroscopyModel: TFS TITAN THEMIS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 9276

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4particle selection
2cryoSPARC4image acquisition
4cryoSPARC4CTF correction
7PHENIXmodel fitting
9cryoSPARCinitial Euler assignment
10cryoSPARCfinal Euler assignment
12cryoSPARC3D reconstruction
13PHENIXmodel refinement
CTF correctionType: NONE
Particle selectionNum. of particles selected: 812192
3D reconstructionResolution: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 138350 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 82.15 / Protocol: RIGID BODY FIT / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 82.22 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00254435
ELECTRON MICROSCOPYf_angle_d0.63866051
ELECTRON MICROSCOPYf_chiral_restr0.0429682
ELECTRON MICROSCOPYf_plane_restr0.0049786
ELECTRON MICROSCOPYf_dihedral_angle_d7.207639

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