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- PDB-9xb8: ATP-dependent diazotase Mco01_40450 -

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Basic information

Entry
Database: PDB / ID: 9xb8
TitleATP-dependent diazotase Mco01_40450
ComponentsFatty-acid-CoA ligase FadD
KeywordsLIGASE / diazotase / enzyme / ATP-dependent
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsNing, J. / Kawai, S. / Ohnishi, Y. / Katsuyama, 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 23, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fatty-acid-CoA ligase FadD
B: Fatty-acid-CoA ligase FadD
C: Fatty-acid-CoA ligase FadD
D: Fatty-acid-CoA ligase FadD


Theoretical massNumber of molelcules
Total (without water)253,0674
Polymers253,0674
Non-polymers00
Water00
1
A: Fatty-acid-CoA ligase FadD
B: Fatty-acid-CoA ligase FadD


Theoretical massNumber of molelcules
Total (without water)126,5332
Polymers126,5332
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Fatty-acid-CoA ligase FadD
D: Fatty-acid-CoA ligase FadD


Theoretical massNumber of molelcules
Total (without water)126,5332
Polymers126,5332
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.193, 163.993, 107.686
Angle α, β, γ (deg.)90.000, 99.708, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Fatty-acid-CoA ligase FadD / ATP-dependent diazotase Mco01_40450


Mass: 63266.629 Da / Num. of mol.: 4
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
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20% (w/v) PEG 8000, 100 mM imidazole/hydrochloric acid (pH6.5), and 3% (v/v) MPD 2-methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.013 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jul 6, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.013 Å / Relative weight: 1
ReflectionResolution: 3.4→49.01 Å / Num. obs: 28803 / % possible obs: 100 % / Redundancy: 7.1 % / Biso Wilson estimate: 47.22 Å2 / CC1/2: 0.974 / Net I/σ(I): 8.3
Reflection shellResolution: 3.4→3.61 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 2.4 / Num. unique obs: 4632 / CC1/2: 0.754 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.4→49.01 Å / SU ML: 0.4281 / Cross valid method: FREE R-VALUE / σ(F): 0.05 / Phase error: 23.3379
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2371 1856 6.9 %
Rwork0.1544 25024 -
obs0.1602 26880 93.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.47 Å2
Refinement stepCycle: LAST / Resolution: 3.4→49.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13384 0 0 0 13384
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009113728
X-RAY DIFFRACTIONf_angle_d1.066518736
X-RAY DIFFRACTIONf_chiral_restr0.05112096
X-RAY DIFFRACTIONf_plane_restr0.00992444
X-RAY DIFFRACTIONf_dihedral_angle_d15.95854972
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.490.32041200.23071687X-RAY DIFFRACTION83.7
3.49-3.590.30851370.20011858X-RAY DIFFRACTION88.67
3.59-3.710.27831320.19041775X-RAY DIFFRACTION87.32
3.71-3.840.281340.17571870X-RAY DIFFRACTION90.11
3.84-40.25241430.16791897X-RAY DIFFRACTION92.85
4-4.180.24831430.16291918X-RAY DIFFRACTION93.6
4.18-4.40.22331460.13381967X-RAY DIFFRACTION94.84
4.4-4.670.21411440.12731980X-RAY DIFFRACTION96.11
4.67-5.030.20211510.12811977X-RAY DIFFRACTION96.77
5.04-5.540.23891480.14562011X-RAY DIFFRACTION96.9
5.54-6.340.24821500.16241984X-RAY DIFFRACTION96.43
6.34-7.980.19871500.14242018X-RAY DIFFRACTION97.92
7.99-49.010.18291580.12442082X-RAY DIFFRACTION98.63

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