[English] 日本語
Yorodumi
- EMDB-66710: ATP-dependent diazotase Mco01_40450 binding with substrate -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-66710
TitleATP-dependent diazotase Mco01_40450 binding with substrate
Map data
Sample
  • Complex: Monomer of Mco01_40450 binding with substrates
    • Protein or peptide: Fatty-acid-CoA ligase FadD
  • Ligand: ADENOSINE MONOPHOSPHATE
  • Ligand: DIPHOSPHATE
  • Ligand: 4-AMINOHYDROCINNAMIC ACID
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: 3.16 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

-
Structure visualization

Supplemental images

emd_66710.png

Downloads & links

-
Map

FileDownload / File: emd_66710.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.75 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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.75 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.071540356 - 0.15255204
Average (Standard dev.)-0.000070132744 (±0.002598262)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Mask #1

Fileemd_66710_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_66710_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_66710_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Monomer of Mco01_40450 binding with substrates

EntireName: Monomer of Mco01_40450 binding with substrates
Components
  • Complex: Monomer of Mco01_40450 binding with substrates
    • Protein or peptide: Fatty-acid-CoA ligase FadD
  • Ligand: ADENOSINE MONOPHOSPHATE
  • Ligand: DIPHOSPHATE
  • Ligand: 4-AMINOHYDROCINNAMIC ACID

-
Supramolecule #1: Monomer of Mco01_40450 binding with substrates

SupramoleculeName: Monomer of Mco01_40450 binding with substrates / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Microbispora corallina (bacteria)
Molecular weightTheoretical: 63.2 KDa

-
Macromolecule #1: Fatty-acid-CoA ligase FadD

MacromoleculeName: Fatty-acid-CoA ligase FadD / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Microbispora corallina (bacteria)
Molecular weightTheoretical: 63.266629 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MNHKVHHHHH HIEGRHMTLS HETVLTPEQR ARLAADPDLG GGNLLTKAIE ANPHPELPFI HLGRPLTVPS GEQRTELSLL DLDELVQSW SVWYLKQGVR PRDRVAIYLH DSFAYSVHFY ALAQIGAVAV LVNSKASRYI ATELCRQTNP VGVYTDLDHL E ILGEEFHL ...String:
MNHKVHHHHH HIEGRHMTLS HETVLTPEQR ARLAADPDLG GGNLLTKAIE ANPHPELPFI HLGRPLTVPS GEQRTELSLL DLDELVQSW SVWYLKQGVR PRDRVAIYLH DSFAYSVHFY ALAQIGAVAV LVNSKASRYI ATELCRQTNP VGVYTDLDHL E ILGEEFHL LPGLRWTQVA EELPAPPPAK LPQEARFRHV DEDPVSILHS SGTTGRPKPV IQTHRSCVAG PRFRLVDHHE QP GAIMMTA LPQSHLGCIA YSTYAVLGGT PLVPWYDTSG PELAKAVEKY RPTTVMAFGH AYAELAAADL PAGAIDSVNV WIS IGDAVH EKHIKTILGM RSADRAPASF FDRLGTTELG WGVLLKVRTL ADERNDRCVG KPVGVAEVAV LRRDGTEADV NEVG LLGAK GPAITAGYWS DSDTTYRSKL SGFWLTGDMA YRDEAGNYFQ VDRAVDAIET PTGTGYSVFM EELMLNELPE VLDVA VVAG IHRGRTAPVA VVTSSAARPD AQKLLNEANE ALRAAGHPEL TMLEVARSEE DFPVGVTGKV LKRRLREKYS SLSTYI REG GGKSIGTILN DVFV

UniProtKB: Fatty-acid-CoA ligase FadD

-
Macromolecule #2: ADENOSINE MONOPHOSPHATE

MacromoleculeName: ADENOSINE MONOPHOSPHATE / type: ligand / ID: 2 / Number of copies: 1 / Formula: AMP
Molecular weightTheoretical: 347.221 Da
Chemical component information

ChemComp-AMP:
ADENOSINE MONOPHOSPHATE / AMP*YM

-
Macromolecule #3: DIPHOSPHATE

MacromoleculeName: DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 1 / Formula: DPO
Molecular weightTheoretical: 173.943 Da
Chemical component information

ChemComp-DPO:
DIPHOSPHATE

-
Macromolecule #4: 4-AMINOHYDROCINNAMIC ACID

MacromoleculeName: 4-AMINOHYDROCINNAMIC ACID / type: ligand / ID: 4 / Number of copies: 1 / Formula: AHC
Molecular weightTheoretical: 165.189 Da
Chemical component information

ChemComp-AHC:
4-AMINOHYDROCINNAMIC ACID

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
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
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 5 sec. / Pretreatment - Pressure: 0.015 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 291 K / Instrument: FEI VITROBOT MARK IV

-
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

+
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 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 138350
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 82.15
Output model

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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more