8Z15 | pdb_00008z15

Crystal structure of DiatB-NADP-6-DMAIAOx complex

• PDB DOI: https://doi.org/10.2210/pdb8Z15/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Streptomyces ardesiacus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-04-10 Released: 2025-02-19 
• Deposition Author(s): Peng, M., Wu, Q.L.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 
  0.293 (Depositor), 0.293 (DCC) 
• R-Value Work: 
  0.264 (Depositor), 0.265 (DCC) 
• R-Value Observed: 
  0.267 (Depositor) 

Starting Model: in silico

Literature

Bacterial Biosynthesis of Nitrile-Containing Natural Products: Basis for Recognition of Diversified Substrates

Peng, M., Wu, Q., Ma, L., Teng, Z.J., Hou, X., Zhu, H., Ju, J.

(2024) ACS Catal 14: 17780-17793

• DOI: https://doi.org/10.1021/acscatal.4c06581

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 48.63 kDa 
• Atom Count: 3,403 
• Modeled Residue Count: 426 
• Deposited Residue Count: 432 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Flavin-dependent monooxygenase	A	432	Streptomyces ardesiacus	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	B [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
NAP	C [auth A]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
A1D7V	D [auth A]	(~{N}~{Z})-~{N}-[2-[6-(3-methylbut-2-enyl)-1~{H}-indol-3-yl]ethylidene]hydroxylamine C15 H18 N2 O DBTCDTYONKJKNS-IUXPMGMMSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free:  0.293 (Depositor), 0.293 (DCC) 
• R-Value Work:  0.264 (Depositor), 0.265 (DCC) 
• R-Value Observed: 0.267 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.623	α = 90
b = 66.623	β = 90
c = 374.184	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-02-19 
Deposition Author(s): Peng, M., Wu, Q.L.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2025-02-19
  Type: Initial release